rnasplice

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

https://github.com/nf-core/rnasplice

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 10 DOI reference(s) in README
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Academic publication links
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (7.1%) to scientific vocabulary

Keywords

alternative-splicing nextflow nf-core pipeline rna rna-seq splicing workflow

Keywords from Contributors

metagenomics

Last synced: 6 months ago · JSON representation ·

Repository

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Nextflow
Default Branch: master
Homepage: https://nf-co.re/rnasplice
Size: 160 MB

Statistics

Stars: 54
Watchers: 168
Forks: 32
Open Issues: 16
Releases: 5

Topics

alternative-splicing nextflow nf-core pipeline rna rna-seq splicing workflow

Created over 3 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

Introduction

nf-core/rnasplice is a bioinformatics pipeline for alternative splicing analysis of RNA sequencing data obtained from organisms with a reference genome and annotation.

nf-core/rnasplice metro map

Merge re-sequenced FastQ files (cat)
Read QC (FastQC)
Adapter and quality trimming (TrimGalore)
Alignment with STAR
Choice of quantification depending on analysis type:
1. STAR -> Salmon
2. STAR -> featureCounts
3. STAR -> HTSeq (DEXSeq count)
Sort and index alignments (SAMtools)
Create bigWig coverage files (BEDTools, bedGraphToBigWig)
Pseudo-alignment and quantification (Salmon; optional)
Summarize QC (MultiQC)
Differential Exon Usage (DEU):
1. HTSeq -> DEXSeq
2. featureCounts -> edgeR
3. Quantification with featureCounts or HTSeq
4. Differential exon usage with DEXSeq or edgeR
Differential Transcript Usage (DTU):
1. Salmon -> DRIMSeq -> DEXSeq
2. Filtering with DRIMSeq
3. Differential transcript usage with DEXSeq
Event-based splicing analysis:
1. STAR -> rMATS
2. Salmon -> SUPPA2

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,fastq_1,fastq_2,strandedness,condition CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,forward,CONTROL CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,forward,CONTROL CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,forward,CONTROL

Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Rows with the same sample identifier are considered technical replicates and merged automatically. The strandedness refers to the library preparation and should be specified by the user.

:::warning Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs. :::

Now, you can run the pipeline using:

bash nextflow run nf-core/rnasplice \ --input samplesheet.csv \ --contrasts contrastsheet.csv \ --genome GRCh37 \ --outdir <OUTDIR> \ -profile <docker/singularity/.../institute>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Online videos

You can find numerous talks on the nf-core events page from various topics including writing pipelines/modules in Nextflow DSL2, using nf-core tooling, running nf-core pipelines as well as more generic content like contributing to Github. Please check them out!

Credits

nf-core/rnasplice was originally written by the bioinformatics team from Zifo RnD Solutions:

We thank Harshil Patel (@drpatelh) and Seqera Labs (seqeralabs) for their assistance in the development of this pipeline.

Zifo RnD Solutions

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #rnasplice channel (you can join with this invite).

Citations

If you use nf-core/rnasplice for your analysis, please cite it using the following doi: 10.5281/zenodo.8424632

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

Name: nf-core
Login: nf-core
Kind: organization
Email: core@nf-co.re

Website: http://nf-co.re
Twitter: nf_core
Repositories: 84
Profile: https://github.com/nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md)

# nf-core/rnasplice: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)

  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [featureCounts](https://academic.oup.com/bioinformatics/article/30/7/923/232889?login=false)

  > Yang Liao, Gordon K. Smyth, Wei Shi, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, Volume 30, Issue 7, 1 April 2014, Pages 923–930.

- [gffread](https://github.com/gpertea/gffread)

- [HTSeq](https://htseq.readthedocs.io/en/master/)

  > Givanna H Putri, Simon Anders, Paul Theodor Pyl, John E Pimanda, Fabio Zanini, Analysing high-throughput sequencing data in Python with HTSeq 2.0, Bioinformatics, Volume 38, Issue 10, 15 May 2022, Pages 2943–2945.

- [MISO](https://miso.readthedocs.io/en/fastmiso/#)

  > Katz Y, Wang ET, Airoldi EM, Burge CB. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods 7, 1009-1015.

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [rMats](https://github.com/Xinglab/rmats-turbo)

  > Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5593-601. doi: 10.1073/pnas.1419161111. Epub 2014 Dec 5. PMID: 25480548; PMCID: PMC4280593.

- [RSEM](https://pubmed.ncbi.nlm.nih.gov/21816040/)

  > Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323. PMID: 21816040; PMCID: PMC3163565.

- [Salmon](https://pubmed.ncbi.nlm.nih.gov/28263959/)

  > Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. PubMed PMID: 28263959; PubMed Central PMCID: PMC5600148.

- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)

  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.

- [SUPPA2](https://github.com/comprna/SUPPA)

  > Trincado, J.L., Entizne, J.C., Hysenaj, G. et al. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol 19, 40 (2018).

- [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)

- [UCSC tools](https://pubmed.ncbi.nlm.nih.gov/20639541/)

  > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.

## R packages

- [R](https://www.r-project.org/)

  > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

- [DEXSeq](https://bioconductor.org/packages/devel/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#References)

  > Anders S, Reyes A, Huber W (2012). “Detecting differential usage of exons from RNA-seq data.” Genome Research, 22, 4025. doi: 10.1101/gr.133744.111.
  > Reyes A, Anders S, Weatheritt R, Gibson T, Steinmetz L, Huber W (2013). “Drift and conservation of differential exon usage across tissues in primate species.” PNAS, 110, -5. doi: 10.1073/pnas.1307202110.

- [DRIMSeq](https://rdrr.io/bioc/DRIMSeq/man/dmFilter.html)

  > Nowicka M, Robinson MD (2016). “DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics [version 2; referees: 2 approved].” F1000Research, 5(1356). doi: 10.12688/f1000research.8900.2.

- [edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html)

  > Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26(1), 139-140. doi: 10.1093/bioinformatics/btp616.
  > McCarthy DJ, Chen Y, Smyth GK (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), 4288-4297. doi: 10.1093/nar/gks042.
  > Chen Y, Lun AAT, Smyth GK (2016). “From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.” F1000Research, 5, 1438. doi: 10.12688/f1000research.8987.2.

- [StageR](bioconductor.org/packages/release/bioc/html/stageR.html)

  > Van den Berge K, Clement L (2022). stageR: stageR: stage-wise analysis of high throughput gene expression data in R. R package version 1.18.0.

- [tximport](https://bioconductor.org/packages/release/bioc/html/tximport.html)

  > Soneson C, Love MI, Robinson MD (2015). “Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.” F1000Research, 4. doi: 10.12688/f1000research.7563.1.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total

Issues event: 13
Watch event: 8
Delete event: 1
Issue comment event: 31
Push event: 16
Pull request review comment event: 7
Pull request event: 18
Pull request review event: 9
Fork event: 9
Create event: 7

Last Year

Issues event: 13
Watch event: 8
Delete event: 1
Issue comment event: 31
Push event: 16
Pull request review comment event: 7
Pull request event: 18
Pull request review event: 9
Fork event: 9
Create event: 7

Committers

Last synced: over 2 years ago

All Time

Total Commits: 302
Total Committers: 14
Avg Commits per committer: 21.571
Development Distribution Score (DDS): 0.566

Past Year

Commits: 230
Committers: 14
Avg Commits per committer: 16.429
Development Distribution Score (DDS): 0.548

Top Committers

Name	Email	Commits
bensouthgate	b**e@g**m	131
James Ashmore	j**e@z**m	104
valentinoruggieri	v**i@z**m	15
James Ashmore	j**1@i**m	10
claireprince	C**e@z**m	9
Keerthana-Bhaskaran-TG	K**B@z**m	8
asmaali98	a**a@z**m	7
nf-core-bot	c**e@n**e	5
lathikaa	l**m@z**m	5
David Koppstein	d**n@d**e	4
Olga Botvinnik	o**k@b**m	1
maxulysse	m**a@g**m	1
valentinoruggieri	1****i	1
James Ashmore	8****e	1

Committer Domains (Top 20 + Academic)

zifornd.com: 6 bridgebio.com: 1 dkfz.de: 1 nf-co.re: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 26
Total pull requests: 83
Average time to close issues: about 1 month
Average time to close pull requests: 8 days
Total issue authors: 16
Total pull request authors: 9
Average comments per issue: 4.35
Average comments per pull request: 1.01
Merged pull requests: 71
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 7
Pull requests: 4
Average time to close issues: N/A
Average time to close pull requests: about 2 months
Issue authors: 6
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.5
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Issue Authors

amizeranschi (6)
SergioManzano10 (3)
dkoppstein (3)
KTMD-plant (2)
hites77 (2)
FriederikeHanssen (2)
paolo-kunderfranco (2)
torres-HI (2)
mdozmorov (1)
gl9797 (1)
fhausmann (1)
jesseangelis (1)
Jokendo-collab (1)
Motoufiq (1)
bio-info-guy (1)

Pull Request Authors

jma1991 (42)
ghost (22)
nf-core-bot (17)
claire-prince (5)
bensouthgate (4)
asmaali98 (3)
lathikaa (2)
valentinoruggieri (2)
FriederikeHanssen (1)
maxulysse (1)
lpantano (1)
tud03125 (1)
jesseangelis (1)
XanderC137 (1)
edmundmiller (1)

Top Labels

Issue Labels

bug (36) enhancement (8)

Pull Request Labels

bug (1)

Dependencies

.github/workflows/awsfulltest.yml actions

actions/upload-artifact v3 composite
nf-core/tower-action v3 composite

.github/workflows/awstest.yml actions

actions/upload-artifact v3 composite
nf-core/tower-action v3 composite

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

actions/checkout v2 composite
nf-core/setup-nextflow v1 composite

.github/workflows/fix-linting.yml actions

actions/checkout v3 composite
actions/setup-node v2 composite

.github/workflows/linting.yml actions

actions/checkout v2 composite
actions/setup-node v2 composite
actions/setup-python v3 composite
actions/upload-artifact v2 composite
mshick/add-pr-comment v1 composite
nf-core/setup-nextflow v1 composite
psf/black stable composite

.github/workflows/linting_comment.yml actions

dawidd6/action-download-artifact v2 composite
marocchino/sticky-pull-request-comment v2 composite

.github/workflows/clean-up.yml actions

actions/stale v7 composite

modules/nf-core/cat/fastq/meta.yml cpan

modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan

modules/nf-core/custom/getchromsizes/meta.yml cpan

modules/nf-core/fastqc/meta.yml cpan

modules/nf-core/gffread/meta.yml cpan

modules/nf-core/gunzip/meta.yml cpan

modules/nf-core/multiqc/meta.yml cpan

modules/nf-core/rsem/preparereference/meta.yml cpan

modules/nf-core/salmon/index/meta.yml cpan

modules/nf-core/salmon/quant/meta.yml cpan

modules/nf-core/samtools/flagstat/meta.yml cpan

modules/nf-core/samtools/idxstats/meta.yml cpan

modules/nf-core/samtools/index/meta.yml cpan

modules/nf-core/samtools/sort/meta.yml cpan

modules/nf-core/samtools/stats/meta.yml cpan

modules/nf-core/star/align/meta.yml cpan

modules/nf-core/star/genomegenerate/meta.yml cpan

modules/nf-core/subread/featurecounts/meta.yml cpan

modules/nf-core/trimgalore/meta.yml cpan

modules/nf-core/ucsc/bedclip/meta.yml cpan

modules/nf-core/ucsc/bedgraphtobigwig/meta.yml cpan

modules/nf-core/umitools/extract/meta.yml cpan

modules/nf-core/untar/meta.yml cpan

subworkflows/nf-core/bam_sort_stats_samtools/meta.yml cpan

subworkflows/nf-core/bam_stats_samtools/meta.yml cpan

subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml cpan

subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml cpan

pyproject.toml pypi

.github/workflows/release-announcements.yml actions

actions/setup-python v4 composite
rzr/fediverse-action master composite
zentered/bluesky-post-action v0.0.2 composite

modules/nf-core/custom/dumpsoftwareversions/environment.yml pypi

modules/nf-core/fastqc/environment.yml pypi

modules/nf-core/multiqc/environment.yml pypi

rnasplice

Science Score: 57.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Introduction

Usage

Pipeline output

Online videos

Credits

Contributions and Support

Citations

Owner

Citation (CITATIONS.md)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

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Dependencies