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Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model.

Code ↔ Paper

5 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 5 matches · all tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Single-cell RNA-seq data analysis ↔ scripts/Run STARsolo for single-cell RNA-seq data.sh, the whole file · a weak match · score 0.79 · single cell RNA, STARsolo, splice junction, barcode, SJ, seq
  2. [2] § Results › Full-length transcriptome profiling identified novel isoforms in TG tissues ↔ scripts/SQANTI3.sh, the whole file · a weak match · score 0.68 · IsoQuant, reference genome, full length transcriptome, mm10, SQANTI3, M25
  3. [3] § Methods › Long-read processing, isoform annotation, and quality assessment ↔ scripts/SQANTI3.sh, the whole file · a weak match · score 0.67 · IsoQuant, reference genome, mm10, SQANTI3, CAGE, motif
  4. [4] § Results › Single-cell splice-junction profiling reveals cell type–restricted usage of novel isoforms in TG ↔ scripts/Run STARsolo for single-cell RNA-seq data.sh, the whole file · a weak match · score 0.62 · single cell, STARsolo, splice junction, SJ, seq, gene
  5. [5] § Results › Full-length transcriptome profiling identified novel isoforms in TG tissues ↔ scripts/isoquant.sh, the whole file · a weak match · score 0.57 · full length transcriptome, IsoQuant, PBS, PacBio, HiFi, Matches

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Shell · 32 lines · 1.1 KB · no license · 2 matches

  1. #!/bin/bash
  2. # Script: Run STARsolo for single-cell RNA-seq data.sh
  3. # Description: Run STARsolo for single-cell RNA-seq BAM file to obtaining splice junction information from single-cell data
  5. # User-configurable variables
  6. THREADS=80
  7. GENOME_DIR="/path/to/STAR_index" #STAR index data of the reference genome
  8. INPUT_BAM="/path/to/possorted_genome_bam.bam" # BAM file of the single-cell RNA-seq data
  9. WHITELIST="/path/to/737K-august-2016.txt" # Barcode whitelist file
  10. OUTPUT_DIR="./SRR11925964" # Output directory
  12. # Create output directory
  13. mkdir -p "${OUTPUT_DIR}"
  14. cd "${OUTPUT_DIR}" || exit 1
  16. # Run STARsolo
  17. /data/p/bin/STAR \
  18. --runThreadN ${THREADS} \
  19. --genomeDir ${GENOME_DIR} \
  20. --soloType CB_UMI_Simple \
  21. --readFilesIn ${INPUT_BAM} \
  22. --readFilesCommand "samtools view -F 0x100" \
  23. --readFilesType SAM SE \
  24. --soloInputSAMattrBarcodeSeq CR UR \
  25. --soloInputSAMattrBarcodeQual CY UY \
  26. --soloCBwhitelist ${WHITELIST} \
  27. --soloFeatures Gene SJ \
  28. --soloOutFileNames SRR11925964
  30. echo "STARsolo analysis completed. Output saved to: ${OUTPUT_DIR}"
  32. # The above provides a sample running script. You can run other samples by changing the sample.

Run STARsolo for single-cell RNA-seq data.sh at commit fa2489f, no license · at the source

Overview

Authors: Zhiyao Han1, Beirui Yu2, Maoqia Shen1, Ziyuan Tang1, Xinran Li1, Mingyang Wang1, Fengxian Li1,3, Xiaolong Cao1,4
ORCID iDs: Fengxian Li, Xiaolong Cao
  1. Department of Anesthesiology, Institute of Perioperative and Organ Protection, Zhujiang Hospital, Southern Medical University,Guangzhou, China
  2. Department of Oncology, Zhujiang Hospital, Southern Medical University,Guangzhou, China
  3. Key Laboratory of Mental Health of the Ministry of Education, Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University,Guangzhou, China
  4. Translational Medicine Research Center, Zhujiang Hospital, Southern Medical University,Guangzhou, China
Institutions: Southern Medical University (China)
Journal: BMC genomics, volume 27, issue 1, article 768
Dates: received 17 November 2025; accepted 2 June 2026; published online 30 July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1186/s12864-026-13024-y · PMID 42760511 · PMCID PMC13589356 · OpenAlex W7171815254
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), mouse (organism), cellular / molecular (subfield)
Methods: Smoothing, state filtering, decompositions, Spectral & time-frequency
Keywords: Allergic rhinitis, Full-length, Novel isoforms, Transcriptomes, Trigeminal ganglion
MeSH: Rhinitis, Allergic*, RNA-Seq*, Trigeminal Ganglion*, Alternative Splicing, Animals, Disease Models, Animal, Gene Expression Profiling, Mice, Protein Isoforms, Transcriptome (* major topic)
Topic: Allergic Rhinitis and Sensitization (Immunology and Allergy, Medicine), according to OpenAlex
Funding: ational Science Foundation of China (82471252); Guangdong Basic and Applied Basic Research Foundation (2024A1515010594); National Science Foundation of China (32200528)
Citations: not cited yet (Europe PMC); 41 references in the paper

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

Its files are read in the Code ↔ Paper reader above, with 5 matches between paragraphs and lines of code.

yerry77/TG-full-length

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: fa2489f0bb498a8e96a6ef205c56d120664f3473, 14 January 2026
Languages: R (3), Shell (3)
Size: 15 files, 6 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (3 files), tidyverse (3 files), circlize (1 file), clusterProfiler (1 file), ComplexHeatmap (1 file), patchwork (1 file), Seurat (1 file), STAR (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
7 files
At the source: github.com/yerry77/TG-full-length

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 6 scripts, each with its path and the digest of its content;
  • 5 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1186/s12864-026-13024-y.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 8 authors, 5 keywords, 10 MeSH terms, 3 funders, 39 references.

Cite

This paper

Han, Z., Yu, B., Shen, M., Tang, Z., Li, X., Wang, M., Li, F., & Cao, X. (2026). Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model. BMC genomics, 27(1), 768. https://doi.org/10.1186/s12864-026-13024-y

BibTeX

@article{han2026long,
author = {Han, Zhiyao and Yu, Beirui and Shen, Maoqia and Tang, Ziyuan and Li, Xinran and Wang, Mingyang and Li, Fengxian and Cao, Xiaolong},
title = {{Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model}},
journal = {BMC genomics},
year = {2026},
month = jul,
volume = {27},
number = {1},
pages = {768},
publisher = {BMC},
issn = {1471-2164},
doi = {10.1186/s12864-026-13024-y},
url = {https://doi.org/10.1186/s12864-026-13024-y},
pmid = {42760511},
pmcid = {PMC13589356}
}

RIS

TY - JOUR
AU - Han, Zhiyao
AU - Yu, Beirui
AU - Shen, Maoqia
AU - Tang, Ziyuan
AU - Li, Xinran
AU - Wang, Mingyang
AU - Li, Fengxian
AU - Cao, Xiaolong
TI - Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model
T2 - BMC genomics
J2 - BMC Genomics
PY - 2026
DA - 2026/07/30
VL - 27
IS - 1
SP - 768
SN - 1471-2164
PB - BMC
DO - 10.1186/s12864-026-13024-y
UR - https://doi.org/10.1186/s12864-026-13024-y
LA - en
ER -

CSL-JSON

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"type": "article-journal",
"title": "Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model",
"container-title": "BMC genomics",
"author": [
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"family": "Han",
"given": "Zhiyao"
},
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"ISSN": "1471-2164",
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"issued": {
"date-parts": [
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2026,
7,
30
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]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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