Data

Tools

Indexes

Applications

Experiments

Open Source Science

rnaseq

https://github.com/singleron-rd/rnaseq

Science Score: 44.0%

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
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.3%) to scientific vocabulary
Last synced: 9 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: singleron-RD
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 5.46 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created about 2 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

singleron-RD/rnaseq: Usage

This pipeline is modified based on nf-core/rnaseq 3.14.0 to analyze accuraSCOPE RNA data.

First, split the FASTQ files into individual wells (cells), and then treat each well as a separate sample to run the nf-core/rnaseq pipeline.

Usage

bash nextflow run singleron-RD/rnaseq \ -params-file params.yaml -profile docker -bg -resume

params.yaml yaml input: 'samplesheet.csv' fasta: /genomePath/Mus_musculus.GRCm39.dna.primary_assembly.fa gtf: /genomePath/Mus_musculus.GRCm39.110.gtf star_index: /starIndexPath/ well_sample: /wellSamplePath/well_sample.tsv outdir: outs max_cpus: 24 skip_stringtie: true skip_bigwig: true skip_fastqc: true skip_trimming: true

well-sample

(Required): A TSV file path(must be absolute path) containing well numbers and sample names of wells.

Columns:
1st column: Well numbers
2nd column: Corresponding sample names

Example: tsv 25 cell25 26 cell26 27 cell27 28 cell28 29 cell29 30 cell30 31 cell31

samplesheet.csv csv sample,fastq_1,fastq_2,strandedness test1,/fastqPath/AEG588A1_S1_L001_R1_001.fastq.gz,/fastqPath/AEG588A1_S1_L001_R2_001.fastq.gz,auto test1,/fastqPath/AEG588A1_S1_L002_R1_001.fastq.gz,/fastqPath/AEG588A1_S1_L002_R2_001.fastq.gz,auto Each row represents a pair of fastq files (paired end). Rows with the same sample identifier are considered technical replicates and merged automatically.

Output

In the split directory, the following FASTQ files and metric files are included:

  • signal/*.fq.gz: Reads belonging to sample wells (as defined in the well_sample.tsv file)
  • noise/*.fq.gz: Reads from other wells

  • *_metrics.txt: Overall read count metrics

    • total_reads: Total number of reads in the FASTQ file
    • p3_reads: Number of reads matching the 3′ barcode
    • p5_reads: Number of reads matching the 5′ barcode
    • signal_reads: Reads matching either the 3′ or 5′ barcode and belonging to sample wells

Example: total_reads:100000 p3_reads:40279 (40.28%) p5_reads:58773 (58.77%) signal_reads:98151 (98.15%)

  • *_read_count.tsv: Read counts per well assigned to 3′ and 5′ barcodes

Example:

tsv sample p3 p5 cell30 7106 9596 cell27 7052 9929 cell31 6042 9164 cell28 5588 8067 cell25 4845 6928 cell29 4830 6331 cell26 4807 7866 noise_well_13 3 1 noise_well_75 2 1

For other output files, please refer to the nf-core/rnaseq documentation .

Owner

  • Name: Singleron-R&D
  • Login: singleron-RD
  • Kind: organization

Citation (CITATIONS.md) 

# nf-core/rnaseq: 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

- [BBMap](https://sourceforge.net/projects/bbmap/)

- [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.

- [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/)

  > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.

- [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://pubmed.ncbi.nlm.nih.gov/24227677/)

  > Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.

- [fq](https://github.com/stjude-rust-labs/fq)

- [GffRead](https://pubmed.ncbi.nlm.nih.gov/32489650/)

  > Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. eCollection 2020. PubMed PMID: 32489650; PubMed Central PMCID: PMC7222033.

- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/)

  > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.

- [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.

- [picard-tools](http://broadinstitute.github.io/picard)

- [preseq](https://pubmed.ncbi.nlm.nih.gov/23435259/)

  > Daley T, Smith AD. Predicting the molecular complexity of sequencing libraries. Nat Methods. 2013 Apr;10(4):325-7. doi: 10.1038/nmeth.2375. Epub 2013 Feb 24. PubMed PMID: 23435259; PubMed Central PMCID: PMC3612374.

- [Qualimap 2](https://pubmed.ncbi.nlm.nih.gov/26428292/)

  > Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Bioinformatics. 2016 Jan 15;32(2):292-4. doi: 10.1093/bioinformatics/btv566. Epub 2015 Oct 1. PubMed PMID: 26428292; PubMed Central PMCID: PMC4708105.

- [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. PubMed PMID: 21816040; PubMed Central PMCID: PMC3163565.

- [RSeQC](https://pubmed.ncbi.nlm.nih.gov/22743226/)

  > Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27. PubMed PMID: 22743226.

- [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.

- [SortMeRNA](https://pubmed.ncbi.nlm.nih.gov/23071270/)

  > Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Bioinformatics. 2012 Dec 15;28(24):3211-7. doi: 10.1093/bioinformatics/bts611. Epub 2012 Oct 15. PubMed PMID: 23071270.

- [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.

- [StringTie2](https://pubmed.ncbi.nlm.nih.gov/31842956/)

  > Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988.

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

- [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)

  > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.

- [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.

- [DESeq2](https://pubmed.ncbi.nlm.nih.gov/25516281/)

  > Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMC4302049.

- [dupRadar](https://pubmed.ncbi.nlm.nih.gov/27769170/)

  > Sayols S, Scherzinger D, Klein H. dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data BMC Bioinformatics. 2016 Oct 21;17(1):428. doi: 10.1186/s12859-016-1276-2. PubMed PMID: 27769170; PubMed Central PMCID: PMC5073875.

- [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)

  > H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.

- [optparse](https://CRAN.R-project.org/package=optparse)

  > Trevor L Davis (2018). optparse: Command Line Option Parser.

- [pheatmap](https://CRAN.R-project.org/package=pheatmap)

  > Raivo Kolde (2018). pheatmap: Pretty Heatmaps.

- [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)

  > Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.

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

  > Morgan M, Obenchain V, Hester J and Pagès H (2020). SummarizedExperiment: SummarizedExperiment container.

- [Tximeta](https://pubmed.ncbi.nlm.nih.gov/32097405/)
  > Love MI, Soneson C, Hickey PF, Johnson LK, Pierce NT, Shepherd L, Morgan M, Patro R. Tximeta: Reference sequence checksums for provenance identification in RNA-seq PLoS Comput Biol. 2020 Feb 25;16(2):e1007664. doi: 10.1371/journal.pcbi.1007664. eCollection 2020 Feb. PubMed PMID: 32097405; PubMed Central PMCID: PMC7059966.

## 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
  • Push event: 2
Last Year
  • Push event: 2

Dependencies

.github/workflows/branch.yml actions
  • mshick/add-pr-comment b8f338c590a895d50bcbfa6c5859251edc8952fc composite
.github/workflows/ci.yml actions
  • actions/checkout b4ffde65f46336ab88eb53be808477a3936bae11 composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/download_pipeline.yml actions
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • eWaterCycle/setup-singularity 931d4e31109e875b13309ae1d07c70ca8fbc8537 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout b4ffde65f46336ab88eb53be808477a3936bae11 composite
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • peter-evans/create-or-update-comment 71345be0265236311c031f5c7866368bd1eff043 composite
.github/workflows/linting.yml actions
  • actions/checkout b4ffde65f46336ab88eb53be808477a3936bae11 composite
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
modules/nf-core/bbmap/bbsplit/meta.yml cpan
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/fastp/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/fq/subsample/meta.yml cpan
modules/nf-core/gffread/meta.yml cpan
modules/nf-core/gunzip/meta.yml cpan
modules/nf-core/hisat2/align/meta.yml cpan
modules/nf-core/hisat2/build/meta.yml cpan
modules/nf-core/hisat2/extractsplicesites/meta.yml cpan
modules/nf-core/kallisto/index/meta.yml cpan
modules/nf-core/kallisto/quant/meta.yml cpan
modules/nf-core/picard/markduplicates/meta.yml cpan
modules/nf-core/preseq/lcextrap/meta.yml cpan
modules/nf-core/qualimap/rnaseq/meta.yml cpan
modules/nf-core/rsem/calculateexpression/meta.yml cpan
modules/nf-core/rsem/preparereference/meta.yml cpan
modules/nf-core/rseqc/bamstat/meta.yml cpan
modules/nf-core/rseqc/inferexperiment/meta.yml cpan
modules/nf-core/rseqc/innerdistance/meta.yml cpan
modules/nf-core/rseqc/junctionannotation/meta.yml cpan
modules/nf-core/rseqc/junctionsaturation/meta.yml cpan
modules/nf-core/rseqc/readdistribution/meta.yml cpan
modules/nf-core/rseqc/readduplication/meta.yml cpan
modules/nf-core/rseqc/tin/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/sortmerna/meta.yml cpan
modules/nf-core/star/align/meta.yml cpan
modules/nf-core/star/genomegenerate/meta.yml cpan
modules/nf-core/stringtie/stringtie/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/dedup/meta.yml cpan
modules/nf-core/umitools/extract/meta.yml cpan
modules/nf-core/untar/meta.yml cpan
subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml cpan
subworkflows/nf-core/bam_markduplicates_picard/meta.yml cpan
subworkflows/nf-core/bam_rseqc/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_align_hisat2/meta.yml cpan
subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml cpan
subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml cpan
subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml cpan
pyproject.toml pypi
modules/nf-core/custom/dumpsoftwareversions/environment.yml conda
  • multiqc 1.17.*
modules/nf-core/kallisto/index/environment.yml conda
  • kallisto 0.48.0.*
modules/nf-core/kallisto/quant/environment.yml conda
  • kallisto 0.48.0.*
modules/local/split_well/environment.yml pypi
  • sccore ==0.0.0