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MIF-Induced CD74+ Microglia and Macrophages Promote Progression of Brain Metastasis and Are Clinically Relevant across Central Nervous System Disorders.

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  1. [1] § Materials and Methods › Bulk RNA-seq ↔ RNAseq/RNAseq.pl, lines 485–542 · score 0.65 · fastQC, DESeq2, HTSeq, Bowtie, genome, TopHat

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The authors' code

Perl · 720 lines · 32 KB · CC-BY-NC-ND-4.0 · 1 match

  1. #!/usr/bin/perl -w
  3. # nextpresso
  5. # RNAseq.pl
  6. # Author: Osvaldo Grana
  7. # Description : RNA-seq analysis pipeline
  8. # v1.9.1 oct2017 - creates the temporal directory (tmp) inside the workspace, and not inside the /tmp of the machine
  9. #
  10. # v1.9.2 ene2018 - removes genes with expression levels below background + removes genes with flat pattern expression.
  11. # After this removal, a new GTF is created that contains only those genes that passed the filtering: cuffquant+cuffdiff+cuffnorm
  12. # or htseqcount+deseq is run again using this reduced gene annotation (new GTF)
  13. # (see addings in level 5 and level 6 here, plus the addings in ExecutionLevels.pm
  14. # mar2018 - run.log now appends new contents (instead of writing from scratch again)
  17. my $version="v1.9.2, ene2018";
  20. use strict;
  21. use warnings;
  22. use autodie;
  24. #determines current working directory
  25. #use Cwd qw(cwd);
  26. #my $bin=cwd;
  29. use File::Temp qw(tempdir); #assigns a temp. subdir inside the main temp. dir
  31. use FindBin qw($Bin); #finds out script path
  32. use File::Basename qw(dirname); #calls dirname function to find out the parent dir below
  33. use File::Spec::Functions qw(catdir); #calls catdir function
  35. #loads own packages
  36. use lib catdir(dirname($Bin), 'Utils'); #finds out Utils dir from parent dir
  37. use xmlParRNAseq 'processXML'; #loads modules from Utils
  38. use ExecutionLevels;
  39. use Miscellaneous;
  41. use Getopt::Long; #to get options
  42. #use File::Basename;
  43. use File::Spec;
  44. use File::Path qw(make_path);
  45. use FileHandle;
  47. #use File::Copy;
  48. #use Sys::Hostname;
  50. use Carp qw( confess ); # to verbose stack traces
  51. use Config; # to check if perl was compiled with thread support
  54. #subroutine prototypes
  55. sub main();
  56. sub help();
  57. sub checkProgramPaths($);
  58. sub checkSampleFiles($$);
  60. main(); #calls main function
  63. sub main(){
  65. system("clear");
  66. print "*****************************************************************************\n";
  67. print "* *\n";
  68. print "* nextpresso: next generation sequencing expression analysis pipeline *\n";
  69. print "* ".$version." *\n";
  70. print "* Author: Osvaldo Grana *\n";
  71. print "* *\n";
  72. print "*****************************************************************************\n\n";
  74. #creates a temporal subdirectory in the temporal directory of the machine (like '/tmp')
  75. #with an unrecognized name like ('/tmp/mY0qHO36dP')
  76. # CLEANUP => 1 implies that this subdirectory is removed when the execution finishes
  77. # CLEANUP => 0 implies that this subdirectory is NOT removed when the execution finishes
  78. #my $executionCreatedTempDir = tempdir( CLEANUP => 0 );
  81. #Checks if perl was compiled with thread support
  82. $Config{useithreads} or die("\n\n**** Please recompile Perl with thread support before running nextpresso.\n\n");
  84. # Verbose stack traces
  85. $SIG{__DIE__} = \&confess;
  86. $SIG{__WARN__} = \&confess;
  89. my $level = "1345"; # default value;
  91. my $configXMLSchema = $Bin."config/config.xsd";
  92. my $experimentXMLSchema = $Bin."config/experiment.xsd";
  93. my $configXMLDocument = undef;
  94. my $experimentXMLDocument = undef;
  95. my $Cuffdiff_ONLY_background_and_flatPattern_filtering=0;
  96. my $DESeq2_ONLY_background_and_flatPattern_filtering=0;
  98. GetOptions(
  99. "configDoc=s"=>\$configXMLDocument, #string
  100. "expDoc=s"=>\$experimentXMLDocument, #string
  101. "step=i"=>\$level, #numeric
  102. "Cuffdiff_ONLY_background_and_flatPattern_filtering" =>\$Cuffdiff_ONLY_background_and_flatPattern_filtering,
  103. "DESeq2_ONLY_background_and_flatPattern_filtering" =>\$DESeq2_ONLY_background_and_flatPattern_filtering
  104. );
  107. #it always checks level 0
  108. $level="0".$level;
  110. if(defined($configXMLDocument) && defined($configXMLDocument)){
  111. if((!-e $configXMLSchema) || (!-e $configXMLDocument) || (!-e $experimentXMLSchema) || (!-e $experimentXMLDocument)){
  112. print "**** One or several of the following files do not exist:\n\n";
  113. print "File 1: ".$configXMLSchema."\nFile 2: ".$configXMLDocument."\nFile 3: ".$experimentXMLSchema."\nFile 4: ".$experimentXMLDocument."\n";
  114. print "\n[Execution finished]\n\n";
  116. help();
  117. }
  118. }else{
  119. help();
  120. }
  123. #<------------- GETS THE DATA FROM THE XML DOCUMENTS ------------->
  124. #validates XML documents and returns them as hash tables
  125. my $configHashRef=xmlParRNAseq::processXML($configXMLSchema, $configXMLDocument);
  126. my $experimentHashRef=xmlParRNAseq::processXML($experimentXMLSchema, $experimentXMLDocument);
  128. #returns a new hash ref, with "/" added at the end of path lines in the case it was not present
  129. $configHashRef=checkProgramPaths($configHashRef);
  132. #getting config info
  133. my $fastQCpath=${$configHashRef}{fastQCpath}[0];
  134. my $fastQScreenPath=${$configHashRef}{fastQScreen}[0]{path}[0];
  135. my $fastQScreenConf=${$configHashRef}{fastQScreen}[0]{configurationFile}[0];
  136. my $fastQScreenSubset=${$configHashRef}{fastQScreen}[0]{subset}[0];
  137. my $bedtoolsPath=${$configHashRef}{bedtoolsPath}[0];
  138. my $samtoolsPath=${$configHashRef}{samtoolsPath}[0];
  139. my $bowtiePath=${$configHashRef}{bowtiePath}[0];
  140. my $tophatPath=${$configHashRef}{tophatPath}[0];
  141. my $peakAnnotatorPath=${$configHashRef}{peakAnnotatorPath}[0];
  142. my $htseqCountPath=${$configHashRef}{htseqCount}[0]{path}[0];
  143. my $htseqCountPythonpath=${$configHashRef}{htseqCount}[0]{pythonpath}[0];
  144. my $tophatFusion=${$configHashRef}{tophatFusion}[0]{path}[0];
  145. my $cufflinksPath=${$configHashRef}{cufflinks}[0]{path}[0];
  146. my $bedGraphToBigWigPath=${$configHashRef}{bedGraphToBigWig}[0]{path}[0];
  147. my $maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep=${$configHashRef}{maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep};
  148. my $seqtkPath=${$configHashRef}{seqtk}[0]{path}[0];
  149. my $seqtk_maximunNumberOfInstancesForDownSampling=${$configHashRef}{seqtk}[0]{maximunNumberOfInstancesForDownSampling}[0];
  150. my $queueSystem=${$configHashRef}{queueSystem}[0];
  151. my $queueName=${$configHashRef}{queueName}[0];
  152. my $multicore=${$configHashRef}{multicore}[0];
  153. my $perl5lib=${$configHashRef}{PERL5LIB}[0];
  154. my $gseaPath=${$configHashRef}{gsea}[0]{path}[0];
  155. my $gseaChip=${$configHashRef}{gsea}[0]{chip}[0];
  156. my $gseamaxMemory=${$configHashRef}{gsea}[0]{maxMemory}[0];
  157. my $extraPathsRequired=${$configHashRef}{extraPathsRequired}[0];
  158. if($extraPathsRequired=~ /HASH\(/){$extraPathsRequired="NO_EXTRA_PATHS"}
  160. #getting experiment info
  161. my $experimentName=${$experimentHashRef}{projectName};
  162. my $queueProject=$experimentName;
  165. my $workspace=${$experimentHashRef}{workspace};
  166. #creates a temporal directory
  167. my $executionCreatedTempDir=$workspace."/tmp/".$experimentName;
  168. my $initialTimeANDdate=Miscellaneous::getCurrentDateAndTime();
  169. $initialTimeANDdate=~ s/ //g;
  170. my $temporaryFilesPrefix=$initialTimeANDdate;
  171. $temporaryFilesPrefix=~ s/\[//;
  172. $temporaryFilesPrefix=~ s/\]//;
  173. $temporaryFilesPrefix=~ s/-//g;
  174. $temporaryFilesPrefix=~ s/,/_/;
  175. $temporaryFilesPrefix=~ s/\:/-/g;
  176. $executionCreatedTempDir.="_".$temporaryFilesPrefix;
  178. #removes it and create it again
  179. File::Path::make_path($executionCreatedTempDir,$executionCreatedTempDir);
  185. my $referenceSequence=${$experimentHashRef}{referenceSequence};
  186. my $indexPrefixForReferenceSequence=${$experimentHashRef}{referenceSequence};
  187. $indexPrefixForReferenceSequence=~ s/\.fa$//;
  188. $indexPrefixForReferenceSequence=~ s/\.fasta$//;
  189. my $GTF=${$experimentHashRef}{GTF};
  190. # one copy of the original GTF is preserved below in mind (initialGTF). This is valid when having spikes in the created annotation.
  191. # It is more appropriated, in this case, to run htseqcount and cuffdiff withou including spikes in the GTF annotation,
  192. # as their quantification values could affect and modify FPKM normalization for the rest of the genes.
  193. my $initialGTF=$GTF;
  194. my $samples=${$experimentHashRef}{library}; # hashRef
  195. my $comparisons=${$experimentHashRef}{comparison}; # hashRef
  196. my $tophatParams=${$experimentHashRef}{tophat}; # hashRef
  197. my $pairedEnd=${$experimentHashRef}{pairedEnd};
  198. my $fileWithChecksumCodesToValidate=${$experimentHashRef}{fileWithChecksumCodesToValidate};
  199. my $cufflinksParams=${$experimentHashRef}{cufflinks}; # hashRef
  200. my $cuffmergeParams=${$experimentHashRef}{cuffmerge}; # hashRef
  201. my $cuffquantParams=${$experimentHashRef}{cuffquant}; # hashRef
  202. my $cuffnormParams=${$experimentHashRef}{cuffnorm}; # hashRef
  203. my $cuffdiffParams=${$experimentHashRef}{cuffdiff}; # hashRef
  204. my $htseqcountParams=${$experimentHashRef}{htseqcount}; # hashRef
  205. my $deseqParams=${$experimentHashRef}{deseq2};
  206. my $bedGraphToBigWigParams=${$experimentHashRef}{bedGraphToBigWig};
  207. my $gseaParams=${$experimentHashRef}{gsea};
  208. my $tophatfusionParams=${$experimentHashRef}{tophatfusion};
  209. my $spikeInControlMixesParams=${$experimentHashRef}{spikeInControlMixes};
  210. my $doSpikesAndGenomeRefIndexing=lc($spikeInControlMixesParams->[0]->{do});
  212. #checks that the sample files exist
  213. checkSampleFiles($pairedEnd,$samples);
  216. # <----------------- only for testing ----------------------->
  217. #use Data::Dumper;
  218. #print STDERR "FILE:\n".Dumper($experimentHashRef)."\n";
  222. #<------------- ANALYSIS OF THE DATA STARTS ------------->
  226. if (! File::Spec->file_name_is_absolute($workspace)){
  227. print STDERR "\n[ERROR]: Incorrect absolute path for output directory: $workspace\n\n";
  228. exit(-1);
  229. }
  231. # the workspace directory is created
  232. if($workspace!~ /\/$/){
  233. $workspace.="/";
  234. }
  235. File::Path::make_path($workspace);
  237. if(!-d $workspace){
  238. print STDERR "\n[ERROR]: Cannot create workspace $workspace\n\n";
  239. exit(-1);
  240. }
  242. my $logFile=$workspace."run.log";
  243. my $logfh=FileHandle->new(">>".$logFile);
  244. if(!-e $logfh){
  245. print STDERR "\n[ERROR]: Cannot create ".$logfh."\n\n";
  246. exit(-1);
  247. }else{
  248. print $logfh $initialTimeANDdate." RNAseq pipeline: Starting analysis for $experimentName experiment\n";
  249. if(-d $executionCreatedTempDir){
  250. print $logfh (Miscellaneous::getCurrentDateAndTime())."[DONE]: created temporal subdirectory for this execution ".$executionCreatedTempDir."\n";}
  251. else{
  252. print $logfh (Miscellaneous::getCurrentDateAndTime())."[ERROR]: could not create temporal subdirectory for this execution ".$executionCreatedTempDir."\n";
  253. print STDERR "\n[ERROR]: could not create temporal subdirectory for this execution ".$executionCreatedTempDir."\n";
  254. exit(-1);
  255. }
  256. }
  258. ########## level 0: converts raw read bam files to fastq files if needed or/and prepares reference and GTF index files in case of having spike-in control mixes
  259. if($level=~ /0/){
  260. #**** IMPORTANT: since this level is always done, steps within this level are done ONLY if they were not done before.
  261. #**** for example: suppose that the user wants to do differential expression again (adding a new comparison), in this case it wouldn't make sense
  262. #**** to perform again bam files conversion to fastq files or indexing again the reference for spike-in controls, as these steps were already done
  263. #**** with the first execution of the analysis
  265. #**** IMPORTANT: in the case of using spike-in control mixes, the reference file and the GTF file are different and new files,
  266. #**** that's why they are recovered here
  267. ($referenceSequence,$GTF,$indexPrefixForReferenceSequence)=ExecutionLevels::level_0($fileWithChecksumCodesToValidate,$workspace,$experimentName,$logfh,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$spikeInControlMixesParams,$referenceSequence,$GTF,$samples,$bedtoolsPath,$pairedEnd,$bowtiePath,$indexPrefixForReferenceSequence,
  268. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  269. }
  271. ########## level 1: sequencing quality and contamination check ##########
  272. if($level=~ /1/){
  273. ExecutionLevels::level_1($perl5lib,$fastQCpath,$fastQScreenPath,$fastQScreenConf,$bowtiePath,$experimentName,$workspace,$referenceSequence,
  274. $GTF,$samples,$logfh,$executionCreatedTempDir,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$fastQScreenSubset,$pairedEnd,$queueSystem,$queueName,$multicore,$queueProject);
  275. }
  277. ########## level 2: trimming && downsampling ##########
  278. if($level=~ /2/){
  279. ExecutionLevels::level_2($fastQCpath,$fastQScreenPath,$fastQScreenConf,$bowtiePath,$experimentName,$workspace,$referenceSequence,
  280. $GTF,$samples,$logfh,$executionCreatedTempDir,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$fastQScreenSubset,$pairedEnd,$seqtkPath,
  281. $seqtk_maximunNumberOfInstancesForDownSampling,$queueSystem,$queueName,$multicore,$queueProject);
  283. #for those samples that were trimmed, or trimmed & downsampled (but not only downsampled)
  284. #it must perform level1 again
  285. my %auxHash=%$samples; # hash unref
  286. my $auxiliarSamples=\%auxHash; # hash ref again
  288. foreach my $key (keys %$auxiliarSamples){
  289. my $trimming=$auxiliarSamples->{$key}{trimming}[0]{do};
  290. if($trimming eq "false"){
  291. delete $auxiliarSamples->{$key};
  292. }
  293. }
  295. #if the size of the hash %auxiliarSamples==0, i.e., none of the samples required trimming => no additional FASTQC is required
  296. if(keys(%$auxiliarSamples)>0){
  297. ExecutionLevels::level_1($perl5lib,$fastQCpath,$fastQScreenPath,$fastQScreenConf,$bowtiePath,$experimentName,$workspace,$referenceSequence,
  298. $GTF,$auxiliarSamples,$logfh,$executionCreatedTempDir,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$fastQScreenSubset,$pairedEnd,$queueSystem,$queueName,$multicore,$queueProject);
  299. }
  301. }else{
  302. #in case that a previous analysis was done for this experiment, requiring trimming/downsampling for maybe some of the samples,
  303. #and if a new re-analysis is started just after this step (level 3 for example), it implies that the program has to be aware of
  304. #what are the proper trimmed/downsampled samples
  305. ExecutionLevels::changeSampleNamesInCaseTheyWereTrimmedAndOrDownsampledBefore($samples,$workspace,$pairedEnd);
  306. }
  308. ########## level 3: aligning of reads ##########
  309. if($level=~ /3/){
  310. ExecutionLevels::level_3($tophatPath,$bowtiePath,$samtoolsPath,$bedtoolsPath,$peakAnnotatorPath,$referenceSequence,
  311. $indexPrefixForReferenceSequence,$samples,$GTF,$tophatParams,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$workspace,$experimentName,$logfh,
  312. $executionCreatedTempDir,$pairedEnd,$queueSystem,$queueName,$multicore,$queueProject);
  313. }
  315. ########## level 4: transcripts assembly and quantification (cufflinks and cuffmerge) ##########
  316. if($level=~ /4/){
  317. ExecutionLevels::level_4($extraPathsRequired,$spikeInControlMixesParams,$cufflinksPath,$samtoolsPath,
  318. $bedtoolsPath,$referenceSequence,$indexPrefixForReferenceSequence,$samples,$GTF,$cufflinksParams,
  319. $cuffmergeParams,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,
  320. $workspace,$experimentName,$logfh,$executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  321. }
  323. ########## level 5: differential expression (cuffquant, cuffdiff and cuffnorm) ##########
  324. if($level=~ /5/){
  326. my $doItALL=0;
  328. if(!$Cuffdiff_ONLY_background_and_flatPattern_filtering){$doItALL=1}
  329. else{#only background and flat pattern correction
  331. my $cuffdiffOutDir=$workspace."cuffdiff/"; #checks if initial cuffdiff execution was performed
  333. if(!-e $cuffdiffOutDir){
  334. $doItALL=1; #if general/initial cuffdiff execution was NOT performed, it is then mandatory first
  335. }
  336. }
  340. if($doItALL){#it does it all
  342. # Mandatory during the first execution, or if asked for it again
  343. ExecutionLevels::level_5($doSpikesAndGenomeRefIndexing,$initialGTF,$extraPathsRequired,$comparisons,$cufflinksPath,$samtoolsPath,$bedtoolsPath,$referenceSequence,$indexPrefixForReferenceSequence,
  344. $samples,$GTF,$cuffquantParams,$cuffnormParams,$cuffdiffParams,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$workspace,$experimentName,$logfh,
  345. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  347. #removes back ground level genes + flat pattern genes
  348. ExecutionLevels::removeBackgroundLevelGenesANDFlatPatternGenes_for_cuffdiff_branch($cuffnormParams,$initialGTF,$workspace,$logfh);
  350. #executes all again using the reduced GTF (without back ground level genes + without flat pattern genes)
  351. my $originalAlignmentsDir=$workspace."alignments/";
  352. my $new_workspace=$workspace."cuffdiff_backgroundFiltered_AND_flatPatternFiltered/";
  354. # creates a symbolic link to the alignments dir, to emulate its presence in the new workspace directory
  355. my $reducedGTF=$new_workspace."GTF_without_background_AND_flatpatternGenes.gtf";
  356. my $command="ln -s ".$originalAlignmentsDir." ".$new_workspace;
  357. system($command);
  359. ExecutionLevels::level_5($doSpikesAndGenomeRefIndexing,$reducedGTF,$extraPathsRequired,$comparisons,$cufflinksPath,$samtoolsPath,$bedtoolsPath,$referenceSequence,$indexPrefixForReferenceSequence,
  360. $samples,$reducedGTF,$cuffquantParams,$cuffnormParams,$cuffdiffParams,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$new_workspace,$experimentName,$logfh,
  361. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  363. }else{
  365. #removes back ground level genes + flat pattern genes
  366. ExecutionLevels::removeBackgroundLevelGenesANDFlatPatternGenes_for_cuffdiff_branch($cuffnormParams,$initialGTF,$workspace,$logfh);
  368. #executes all again using the reduced GTF (without back ground level genes + without flat pattern genes)
  369. my $originalAlignmentsDir=$workspace."alignments/";
  370. my $new_workspace=$workspace."cuffdiff_backgroundFiltered_AND_flatPatternFiltered/";
  372. # creates a symbolic link to the alignments dir, to emulate its presence in the new workspace directory
  373. my $reducedGTF=$new_workspace."GTF_without_background_AND_flatpatternGenes.gtf";
  374. my $command="ln -s ".$originalAlignmentsDir." ".$new_workspace;
  375. system($command);
  377. ExecutionLevels::level_5($doSpikesAndGenomeRefIndexing,$reducedGTF,$extraPathsRequired,$comparisons,$cufflinksPath,$samtoolsPath,$bedtoolsPath,$referenceSequence,$indexPrefixForReferenceSequence,
  378. $samples,$reducedGTF,$cuffquantParams,$cuffnormParams,$cuffdiffParams,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$new_workspace,$experimentName,$logfh,
  379. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  380. }
  381. }
  383. ########## level 6: runs htseq-count (gets read counts for genes) + DESeq2 differential expression
  384. if($level=~ /6/){
  386. my $doItALL=0;
  388. if(!$DESeq2_ONLY_background_and_flatPattern_filtering){$doItALL=1}
  389. else{#only background and flat pattern correction
  391. my $deseqOutDir=$workspace."deseq/"; #checks if initial DESeq2 execution was performed
  393. if(!-e $deseqOutDir){
  394. $doItALL=1; #if general/initial DESeq2 execution was NOT performed, it is then mandatory first
  395. }
  396. }
  399. if($doItALL){#it does it all
  400. if($doSpikesAndGenomeRefIndexing eq "false"){
  401. ExecutionLevels::level_6($perl5lib,$comparisons,$deseqParams,$extraPathsRequired,$htseqCountPath,$htseqCountPythonpath,$htseqcountParams,$samtoolsPath,$samples,$GTF,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$workspace,$experimentName,$logfh,
  402. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  404. #removes back ground level genes + flat pattern genes
  405. ExecutionLevels::removeBackgroundLevelGenesANDFlatPatternGenes_for_deseq_branch($deseqParams,$GTF,$workspace,$logfh);
  407. #executes all again using the reduced GTF (without back ground level genes + without flat pattern genes)
  408. my $originalAlignmentsDir=$workspace."alignments/";
  409. my $new_workspace=$workspace."deseq_backgroundFiltered_AND_flatPatternFiltered/";
  411. # creates a symbolic link to the alignments dir, to emulate its presence in the new workspace directory
  412. my $reducedGTF=$new_workspace."GTF_without_background_AND_flatpatternGenes.gtf";
  413. my $command="ln -s ".$originalAlignmentsDir." ".$new_workspace;
  414. system($command);
  416. ExecutionLevels::level_6($perl5lib,$comparisons,$deseqParams,$extraPathsRequired,$htseqCountPath,$htseqCountPythonpath,$htseqcountParams,$samtoolsPath,$samples,$reducedGTF,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$new_workspace,$experimentName,$logfh,
  417. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  419. }else{ # when having spikes, it is more appropriate to not consider them for htseqcount as they could affect
  420. # normalization values for regular genes. So in this case, the original GTF is given instead of the
  421. #one with the combined annotation (genes+spikes)
  422. ExecutionLevels::level_6($perl5lib,$comparisons,$deseqParams,$extraPathsRequired,$htseqCountPath,$htseqcountParams,$samtoolsPath,$samples,$initialGTF,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$workspace,$experimentName,$logfh,
  423. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  425. #removes back ground level genes + flat pattern genes
  426. ExecutionLevels::removeBackgroundLevelGenesANDFlatPatternGenes_for_deseq_branch($deseqParams,$initialGTF,$workspace,$logfh);
  428. #executes all again using the reduced GTF (without back ground level genes + without flat pattern genes)
  429. my $originalAlignmentsDir=$workspace."alignments/";
  430. my $new_workspace=$workspace."deseq_backgroundFiltered_AND_flatPatternFiltered/";
  432. # creates a symbolic link to the alignments dir, to emulate its presence in the new workspace directory
  433. my $reducedGTF=$new_workspace."GTF_without_background_AND_flatpatternGenes.gtf";
  434. my $command="ln -s ".$originalAlignmentsDir." ".$new_workspace;
  435. system($command);
  437. ExecutionLevels::level_6($perl5lib,$comparisons,$deseqParams,$extraPathsRequired,$htseqCountPath,$htseqCountPythonpath,$htseqcountParams,$samtoolsPath,$samples,$reducedGTF,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$new_workspace,$experimentName,$logfh,
  438. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  439. }
  441. }#if($doItALL)
  442. else{
  443. if($doSpikesAndGenomeRefIndexing eq "false"){
  445. #removes back ground level genes + flat pattern genes
  446. ExecutionLevels::removeBackgroundLevelGenesANDFlatPatternGenes_for_deseq_branch($deseqParams,$GTF,$workspace,$logfh);
  448. #executes all again using the reduced GTF (without back ground level genes + without flat pattern genes)
  449. my $originalAlignmentsDir=$workspace."alignments/";
  450. my $new_workspace=$workspace."deseq_backgroundFiltered_AND_flatPatternFiltered/";
  452. # creates a symbolic link to the alignments dir, to emulate its presence in the new workspace directory
  453. my $reducedGTF=$new_workspace."GTF_without_background_AND_flatpatternGenes.gtf";
  454. my $command="ln -s ".$originalAlignmentsDir." ".$new_workspace;
  455. system($command);
  457. ExecutionLevels::level_6($perl5lib,$comparisons,$deseqParams,$extraPathsRequired,$htseqCountPath,$htseqCountPythonpath,$htseqcountParams,$samtoolsPath,$samples,$reducedGTF,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$new_workspace,$experimentName,$logfh,
  458. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  461. }else{ # when having spikes, it is more appropriate to not consider them for htseqcount as they could affect
  462. # normalization values for regular genes. So in this case, the original GTF is given instead of the
  463. #one with the combined annotation (genes+spikes)
  465. #removes back ground level genes + flat pattern genes
  466. ExecutionLevels::removeBackgroundLevelGenesANDFlatPatternGenes_for_deseq_branch($deseqParams,$initialGTF,$workspace,$logfh);
  468. #executes all again using the reduced GTF (without back ground level genes + without flat pattern genes)
  469. my $originalAlignmentsDir=$workspace."alignments/";
  470. my $new_workspace=$workspace."deseq_backgroundFiltered_AND_flatPatternFiltered/";
  472. # creates a symbolic link to the alignments dir, to emulate its presence in the new workspace directory
  473. my $reducedGTF=$new_workspace."GTF_without_background_AND_flatpatternGenes.gtf";
  474. my $command="ln -s ".$originalAlignmentsDir." ".$new_workspace;
  475. system($command);
  477. ExecutionLevels::level_6($perl5lib,$comparisons,$deseqParams,$extraPathsRequired,$htseqCountPath,$htseqCountPythonpath,$htseqcountParams,$samtoolsPath,$samples,$reducedGTF,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$new_workspace,$experimentName,$logfh,
  478. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  480. }
  481. }#else #if($doItALL)
  483. }
  485. ########## level 7: creates wiggle files from bam alignments
  486. if($level=~ /7/){
  487. ExecutionLevels::level_7($bedGraphToBigWigPath,$bedGraphToBigWigParams,$bedtoolsPath,$samtoolsPath,$samples,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$workspace,$experimentName,$logfh,
  488. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  489. }
  491. ########## level 8: preRanked GSEA
  492. if($level=~ /8/){
  493. #****rnk files are directly taken from cuffdiff output files
  494. ExecutionLevels::level_8($gseaChip,$gseamaxMemory,$gseaPath,$gseaParams,$workspace,$experimentName,$logfh,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$comparisons,
  495. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  496. }
  498. ########## level 9: gene fusion prediction with Tophat-fusion
  499. if($level=~ /9/){
  500. ExecutionLevels::level_9($tophatfusionParams,$tophatPath,$bowtiePath,$samtoolsPath,$workspace,$experimentName,$logfh,$maximunNumberOfInstancesAllowedToRunSimultaneouslyInOneParticularStep,$samples,$referenceSequence,
  501. $executionCreatedTempDir,$queueSystem,$queueName,$multicore,$queueProject);
  502. }
  504. #close the log file
  505. $logfh->close;
  507. }
  509. sub help(){
  510. my $usage = qq{
  512. perl RNAseq.pl --configDoc configDocFile --expDoc expDocFile --step step_number
  515. Example:
  517. a) complete execution of all steps in each workflow level
  518. perl RNAseq.pl --configDoc config/configurationParameters.xml --expDoc config/experimentParameters.xml --step 123456789
  520. b) execution of some detailed steps
  521. perl RNAseq.pl --configDoc config/configurationParameters.xml --expDoc config/experimentParameters.xml --step 1345
  524. Steps Description:
  526. Step 1: sequencing quality && contamination check (fastQC & fastQScreen)
  527. Step 2: trimming && downsampling (seqtk)
  528. Step 3: Aligning (tophat)
  529. Step 4: transcripts assembly && quantification (cufflinks and cuffmerge)
  530. Step 5: differential expression (cuffquant, cuffdiff and cuffnorm)
  531. Step 6: htseq-count (gets read counts for genes) + DESeq2 differential expression
  532. Step 7: BedGraph and BigWig files for genome browsers
  533. Step 8: GSEA for specific gene sets over the different comparisons done with cuffdiff
  534. Step 9: gene fusion prediction
  539. [Optional parameters]
  541. --Cuffdiff_ONLY_background_and_flatPattern_filtering [allows repeating only the last part of setp 5]
  542. --DESeq2_ONLY_background_and_flatPattern_filtering [allows repeating only the last part of setp 6]
  545. };
  547. print STDERR $usage;
  548. exit(1);
  549. }
  551. sub checkProgramPaths($){
  552. my ($configHashRef) = @_;
  554. if(${$configHashRef}{fastQCpath}[0]!~ /\/$/){
  555. ${$configHashRef}{fastQCpath}[0]=${$configHashRef}{fastQCpath}[0].="/";
  556. }
  557. my $program=${$configHashRef}{fastQCpath}[0]."fastqc";
  558. if (!-e $program){
  559. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  560. exit(-1);
  561. }
  563. if(${$configHashRef}{fastQScreen}[0]{path}[0]!~ /\/$/){
  564. ${$configHashRef}{fastQScreen}[0]{path}[0]=${$configHashRef}{fastQScreen}[0]{path}[0].="/";
  565. }
  566. $program=${$configHashRef}{fastQScreen}[0]{path}[0]."fastq_screen";
  567. if (!-e $program){
  568. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  569. exit(-1);
  570. }
  572. $program=${$configHashRef}{fastQScreen}[0]{configurationFile}[0];
  573. if (!-e $program){
  574. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  575. exit(-1);
  576. }
  578. if(${$configHashRef}{seqtk}[0]{path}[0]!~ /\/$/){
  579. ${$configHashRef}{seqtk}[0]{path}[0]=${$configHashRef}{seqtk}[0]{path}[0].="/";
  580. }
  582. $program=${$configHashRef}{seqtk}[0]{path}[0]."seqtk";
  583. if (!-e $program){
  584. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  585. exit(-1);
  586. }
  588. if(${$configHashRef}{bedtoolsPath}[0]!~ /\/$/){
  589. ${$configHashRef}{bedtoolsPath}[0]=${$configHashRef}{bedtoolsPath}[0].="/";
  590. }
  591. $program=${$configHashRef}{bedtoolsPath}[0]."bedtools";
  592. if (!-e $program){
  593. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  594. exit(-1);
  595. }
  597. if(${$configHashRef}{samtoolsPath}[0]!~ /\/$/){
  598. ${$configHashRef}{samtoolsPath}[0]=${$configHashRef}{samtoolsPath}[0].="/";
  599. }
  600. $program=${$configHashRef}{samtoolsPath}[0]."samtools";
  601. if (!-e $program){
  602. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  603. exit(-1);
  604. }
  606. if(${$configHashRef}{bowtiePath}[0]!~ /\/$/){
  607. ${$configHashRef}{bowtiePath}[0]=${$configHashRef}{bowtiePath}[0].="/";
  608. }
  609. $program=${$configHashRef}{bowtiePath}[0]."bowtie";
  610. if (!-e $program){
  611. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  612. exit(-1);
  613. }
  615. if(${$configHashRef}{tophatPath}[0]!~ /\/$/){
  616. ${$configHashRef}{tophatPath}[0]=${$configHashRef}{tophatPath}[0].="/";
  617. }
  618. $program=${$configHashRef}{tophatPath}[0]."tophat";
  619. if (!-e $program){
  620. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  621. exit(-1);
  622. }
  624. if(${$configHashRef}{htseqCount}[0]{path}[0]!~ /\/$/){
  625. ${$configHashRef}{htseqCount}[0]{path}[0]=${$configHashRef}{htseqCount}[0]{path}[0].="/";
  626. }
  627. $program=${$configHashRef}{htseqCount}[0]{path}[0]."htseq-count";
  628. if (!-e $program){
  629. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  630. exit(-1);
  631. }
  633. if(${$configHashRef}{tophatFusion}[0]{path}[0]!~ /\/$/){
  634. ${$configHashRef}{tophatFusion}[0]{path}[0]=${$configHashRef}{tophatFusion}[0]{path}[0].="/";
  635. }
  636. $program=${$configHashRef}{tophatFusion}[0]{path}[0]."tophat-fusion-post";
  637. if (!-e $program){
  638. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  639. exit(-1);
  640. }
  642. if(${$configHashRef}{cufflinks}[0]{path}[0]!~ /\/$/){
  643. ${$configHashRef}{cufflinks}[0]{path}[0]=${$configHashRef}{cufflinks}[0]{path}[0].="/";
  644. }
  645. $program=${$configHashRef}{cufflinks}[0]{path}[0]."cufflinks";
  646. if (!-e $program){
  647. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  648. exit(-1);
  649. }
  650. $program=${$configHashRef}{cufflinks}[0]{path}[0]."cuffmerge";
  651. if (!-e $program){
  652. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  653. exit(-1);
  654. }
  655. $program=${$configHashRef}{cufflinks}[0]{path}[0]."cuffquant";
  656. if (!-e $program){
  657. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  658. exit(-1);
  659. }$program=${$configHashRef}{cufflinks}[0]{path}[0]."cuffnorm";
  660. if (!-e $program){
  661. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  662. exit(-1);
  663. }$program=${$configHashRef}{cufflinks}[0]{path}[0]."cuffdiff";
  664. if (!-e $program){
  665. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  666. exit(-1);
  667. }
  669. if(${$configHashRef}{bedGraphToBigWig}[0]{path}[0]!~ /\/$/){
  670. ${$configHashRef}{bedGraphToBigWig}[0]{path}[0]=${$configHashRef}{bedGraphToBigWig}[0]{path}[0].="/";
  671. }
  672. $program=${$configHashRef}{bedGraphToBigWig}[0]{path}[0]."bedGraphToBigWig";
  673. if (!-e $program){
  674. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  675. exit(-1);
  676. }
  678. if(${$configHashRef}{peakAnnotatorPath}[0]!~ /\/$/){
  679. ${$configHashRef}{peakAnnotatorPath}[0]=${$configHashRef}{peakAnnotatorPath}[0].="/";
  680. }
  681. $program=${$configHashRef}{peakAnnotatorPath}[0]."PeakAnnotator.jar";
  682. if (!-e $program){
  683. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  684. exit(-1);
  685. }
  687. $program=${$configHashRef}{gsea}[0]{path}[0];
  688. if (!-e $program){
  689. print STDERR "\n[ERROR]: The program ".$program." doesn't exist\n\n";
  690. exit(-1);
  691. }
  692. return($configHashRef);
  693. }
  695. sub checkSampleFiles($$){
  696. my($pairedEnd,$samples)=@_;
  698. foreach my $key (keys %$samples){
  699. my $type=$samples->{$key}{type}[0];
  700. my $leftFastqFile=$samples->{$key}{leftFile};
  702. if(!-e $leftFastqFile){
  703. print STDERR "\n[ERROR]: The left sample file ".$leftFastqFile." doesn't exist\n\n";
  704. exit(-1);
  705. }
  707. #if paired end experiment
  708. if($pairedEnd eq "true"){
  709. my $rightFastqFile=$samples->{$key}{rightFile}[0];
  711. if(!-e $leftFastqFile){
  712. print STDERR "\n[ERROR]: The right sample file ".$rightFastqFile." doesn't exist\n\n";
  713. exit(-1);
  714. }
  715. }
  716. }
  718. }

RNAseq.pl at commit 1b4c1dd, under CC-BY-NC-ND-4.0 · at the source

Overview

Authors: Laura Alvaro-Espinosa1, Angel Marquez-Galera2, Neibla Priego1, Virginia García-Calvo1, Maria Perea-García1, Carolina Hernandez-Oliver1, Diana Retana1, Oliva Sanchez1, Ana de Pablos-Aragoneses1, Pedro García-Gómez1, Osvaldo Graña-Castro3, Óscar Lapuente-Santana3, Laura Serrano-Ron3, Fatima Al-Shahrour3, Ana Cayuela López4, Isabel Peset4, Diego Megías4, Mihaela Ola5, Damir Varešlija5,6, Leonie S Young5,7,8
and 16 other authorsYolanda Martí-Mateos9, Jose A Enríquez9,10, Elena Hernández-Encinas11, Carmen Blanco-Aparicio11, Maria S Soengas12, Juergen Bernhagen13,14,15, Alejandro Antón-Fernández16, Jesús Ávila16, Miguel A Marchena17, Maximiliano Torres17, Fernando de Castro17, Mar Márquez-Ropero18, Amanda Sierra18,19,20, Jose P Lopez-Atalaya2, RENACER Group, Manuel Valiente1
ORCID iDs: Laura Alvaro-Espinosa, Angel Marquez-Galera, Neibla Priego, Virginia García-Calvo, Maria Perea-García, Carolina Hernandez-Oliver, Diana Retana, Oliva Sanchez, Ana de Pablos-Aragoneses, Pedro García-Gómez, Osvaldo Graña-Castro, Óscar Lapuente-Santana, Laura Serrano-Ron, Fatima Al-Shahrour, Ana Cayuela López, Isabel Peset, Diego Megías, Mihaela Ola, Damir Varešlija, Leonie S Young, Yolanda Martí-Mateos, Jose A Enríquez, Elena Hernández-Encinas, Carmen Blanco-Aparicio, Maria S Soengas, Juergen Bernhagen, Alejandro Antón-Fernández, Jesús Ávila, Miguel A Marchena, Maximiliano Torres, Fernando de Castro, Mar Márquez-Ropero, Amanda Sierra, Jose P Lopez-Atalaya, Manuel Valiente
20 affiliations
  1. Brain Metastasis Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
  2. Instituto de Neurociencias (CSIC-UMH), San Juan de Alicante, Spain
  3. Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
  4. Confocal Microscopy Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
  5. Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
  6. The School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
  7. Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
  8. Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland
  9. Functional Genetics of the Oxidative Phosphorylation System (GENOXPHOS), Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
  10. Centro de Investigaciones Biomédicas en Red en Fragilidad y Envejencimiento Saludable (CIBERFES), Madrid, Spain
  11. Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
  12. Melanoma Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
  13. Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
  14. Munich Heart Alliance, Munich, Germany
  15. Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
  16. Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Madrid, Spain
  17. Instituto Cajal-CSIC, Madrid, Spain
  18. Achucarro Basque Center for Neuroscience, University of the Basque Country UPV/EHU, Leioa, Spain
  19. Department of Biochemistry and Molecular Biology, University of the Basque Country UPV/EHU, Leioa, Spain
  20. Ikerbasque Foundation, Bilbao, Spain
Institutions: Spanish National Cancer Research Centre (Spain); Instituto de Neurociencias (Spain); Royal College of Surgeons in Ireland (Ireland); Beaumont Hospital (Ireland); Spanish National Centre for Cardiovascular Research (Spain); Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (Spain); LMU Klinikum (Germany); Munich Cluster for Systems Neurology (Germany); Institut für Schlaganfall- und Demenzforschung (Germany); Ludwig-Maximilians-Universität München (Germany); Consejo Superior de Investigaciones Científicas (Spain); Centro de Biología Molecular Severo Ochoa (Spain); Universidad Autónoma de Madrid (Spain); Instituto Cajal (Spain); University of the Basque Country (Spain); Achucarro Basque Center for Neuroscience (Spain); Ikerbasque (Spain)
Journal: Cancer research, volume 86, issue 13, pages 3249-3269
Dates: received 6 September 2025; accepted 6 March 2026; published online 24 March 2026; in print 2 July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1158/0008-5472.can-25-4018 · PMID 41874311 · PMCID PMC7618953 · OpenAlex W7140232145
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), mouse (organism), other condition (population), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Evoked potentials, Connectivity, fMRI & imaging
MeSH: Antigens, Differentiation, B-Lymphocyte*, Brain Neoplasms*, Central Nervous System Diseases*, Histocompatibility Antigens Class II*, Intramolecular Oxidoreductases*, Macrophage Migration-Inhibitory Factors*, Macrophages*, Microglia*, Animals, Cell Line, Tumor, Disease Progression, Humans, Mice, Tumor Microenvironment (* major topic)
Topic: Macrophage Migration Inhibitory Factor (Immunology, Immunology and Microbiology), according to OpenAlex
Funding: Research Ireland (Researchirel) (20/FFP-P/8597, 23/SPP/11783, 19/FFP/6443); European Molecular Biology Organization (EMBO) (4053); Fundación Ramón Areces (FRA) (CIVP19A5917, CIVP20S10662, CIVP19S8163); Eusko Jaurlaritza (IT1473-22); Ministerio de Ciencia, Innovación y Universidades (MCIU) (SAF2014-57243-R, PID2022-143110OB-I00 and RED2024-153909-E, RTI2018-099357-B-I00, SAF2017-89643-R, and TED2021-131611B-I00, SAF2015-62547-ERC, PID2021-1279880B, RTI2018-102260-B-I00, RTI2018-099267-B-I00 and PID2022-136698OB-I00, PRE2018-083478); Breast Cancer Now (2021JulyPCC1460, 2019AugSF1310); H2020 Future and Emerging Technologies (828972); European Research Council (884699, 864759); Instituto de Salud Carlos III (ISCIII) (AC20/00114); Ministerio de Asuntos Económicos y Transformación Digital, Gobierno de España (BES-2017-081995, RYC-2013-13365); Fundación Científica Asociación Española Contra el Cáncer (AECC) (POSTD19016PRIE, PRYCO234528VALI, TRNSC213878VALI, LABAE19002VALI); Breast Cancer Ireland (BCI) (18239A01); Melanoma Research Alliance (498103); Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERFES) (CB16/10/00282); "la Caixa" Foundation ("la Caixa") (HR23-00051, LCF/BQ/DI17/11620028, LCF/BQ/DI19/11730044); Fondation Leducq (17CVD04); Transcan (Transcan-3) (TRANSCAN2021-203); Alzheimer's Association (AA) (AARG-NTF-24-1304352); Cancer Research Institute (54545); Generalitat Valenciana (PROMETEO/2020/007); Fundació la Marató de TV3 (201906-30-31-32)
Citations: cited by 2 papers (Europe PMC); 75 references in the paper
Notices: A comment on this paper has been published (42388022, from Europe PMC)

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

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osvaldogc/nextpresso1.9.2

License: CC-BY-NC-ND-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 1b4c1dd66013acbfe16266dfe4230340f880da35, 8 March 2018
Languages: Perl (13)
Size: 216 files, 13 scripts
Software Heritage: archived
Found in: the text, “Bulk RNA-seq”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
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15 files
At the source: github.com/osvaldogc/nextpresso1.9.2

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Version 2, 28 September 2026

  • Publisher: n/a → American Association for Cancer Research

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Cite

This paper

Alvaro-Espinosa, L., Marquez-Galera, A., Priego, N., García-Calvo, V., Perea-García, M., Hernandez-Oliver, C., Retana, D., Sanchez, O., de Pablos-Aragoneses, A., García-Gómez, P., Graña-Castro, O., Lapuente-Santana, Ó., Serrano-Ron, L., Al-Shahrour, F., Cayuela López, A., Peset, I., Megías, D., Ola, M., Varešlija, D., . . . Valiente, M. (2026). MIF-Induced CD74+ Microglia and Macrophages Promote Progression of Brain Metastasis and Are Clinically Relevant across Central Nervous System Disorders. Cancer research, 86(13), 3249-3269. https://doi.org/10.1158/0008-5472.can-25-4018

BibTeX

@article{alvaroespinosa2026mif,
author = {Alvaro-Espinosa, Laura and Marquez-Galera, Angel and Priego, Neibla and García-Calvo, Virginia and Perea-García, Maria and Hernandez-Oliver, Carolina and Retana, Diana and Sanchez, Oliva and de Pablos-Aragoneses, Ana and García-Gómez, Pedro and Graña-Castro, Osvaldo and Lapuente-Santana, Óscar and Serrano-Ron, Laura and Al-Shahrour, Fatima and Cayuela López, Ana and Peset, Isabel and Megías, Diego and Ola, Mihaela and Varešlija, Damir and Young, Leonie S and Martí-Mateos, Yolanda and Enríquez, Jose A and Hernández-Encinas, Elena and Blanco-Aparicio, Carmen and Soengas, Maria S and Bernhagen, Juergen and Antón-Fernández, Alejandro and Ávila, Jesús and Marchena, Miguel A and Torres, Maximiliano and de Castro, Fernando and Márquez-Ropero, Mar and Sierra, Amanda and Lopez-Atalaya, Jose P and {RENACER Group} and Valiente, Manuel},
title = {{MIF-Induced CD74+ Microglia and Macrophages Promote Progression of Brain Metastasis and Are Clinically Relevant across Central Nervous System Disorders}},
journal = {Cancer research},
year = {2026},
month = jul,
volume = {86},
number = {13},
pages = {3249--3269},
publisher = {American Association for Cancer Research},
issn = {0008-5472},
doi = {10.1158/0008-5472.can-25-4018},
url = {https://doi.org/10.1158/0008-5472.can-25-4018},
pmid = {41874311},
pmcid = {PMC7618953}
}

RIS

TY - JOUR
AU - Alvaro-Espinosa, Laura
AU - Marquez-Galera, Angel
AU - Priego, Neibla
AU - García-Calvo, Virginia
AU - Perea-García, Maria
AU - Hernandez-Oliver, Carolina
AU - Retana, Diana
AU - Sanchez, Oliva
AU - de Pablos-Aragoneses, Ana
AU - García-Gómez, Pedro
AU - Graña-Castro, Osvaldo
AU - Lapuente-Santana, Óscar
AU - Serrano-Ron, Laura
AU - Al-Shahrour, Fatima
AU - Cayuela López, Ana
AU - Peset, Isabel
AU - Megías, Diego
AU - Ola, Mihaela
AU - Varešlija, Damir
AU - Young, Leonie S
AU - Martí-Mateos, Yolanda
AU - Enríquez, Jose A
AU - Hernández-Encinas, Elena
AU - Blanco-Aparicio, Carmen
AU - Soengas, Maria S
AU - Bernhagen, Juergen
AU - Antón-Fernández, Alejandro
AU - Ávila, Jesús
AU - Marchena, Miguel A
AU - Torres, Maximiliano
AU - de Castro, Fernando
AU - Márquez-Ropero, Mar
AU - Sierra, Amanda
AU - Lopez-Atalaya, Jose P
AU - RENACER Group
AU - Valiente, Manuel
TI - MIF-Induced CD74+ Microglia and Macrophages Promote Progression of Brain Metastasis and Are Clinically Relevant across Central Nervous System Disorders
T2 - Cancer research
J2 - Cancer Res
PY - 2026
DA - 2026/07/01
VL - 86
IS - 13
SP - 3249
EP - 3269
SN - 0008-5472
PB - American Association for Cancer Research
DO - 10.1158/0008-5472.can-25-4018
UR - https://doi.org/10.1158/0008-5472.can-25-4018
LA - en
ER -

CSL-JSON

{
"id": "10.1158/0008-5472.can-25-4018",
"type": "article-journal",
"title": "MIF-Induced CD74+ Microglia and Macrophages Promote Progression of Brain Metastasis and Are Clinically Relevant across Central Nervous System Disorders",
"container-title": "Cancer research",
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"container-title-short": "Cancer Res",
"volume": "86",
"issue": "13",
"page": "3249-3269",
"DOI": "10.1158/0008-5472.can-25-4018",
"PMID": "41874311",
"PMCID": "PMC7618953",
"ISSN": "0008-5472",
"publisher": "American Association for Cancer Research",
"URL": "https://doi.org/10.1158/0008-5472.can-25-4018",
"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
1
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}

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