RNA-seq Tuxedo Modules

Modules available in the RNA-seq Tuxedo Pipeline.

FASTQC

omics_pipe.modules.fastqc.fastqc(sample, fastqc_flag)

QC check of raw .fastq files using FASTQC.

input:

.fastq file

output:

folder and zipped folder containing html, txt and image files

citation:

Babraham Bioinformatics

link:

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

parameters from parameters file:

RAW_DATA_DIR:

QC_PATH:

FASTQC_VERSION:

COMPRESSION:

TopHat

omics_pipe.modules.tophat.tophat(sample, tophat_flag)

Runs TopHat to align .fastq files.

input:

.fastq file

output:

accepted_hits.bam

citation:

Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics doi:10.1093/bioinformatics/btp120

link:

http://tophat.cbcb.umd.edu/

parameters from parameters file:

RAW_DATA_DIR:

REF_GENES:

TOPHAT_RESULTS:

BOWTIE_INDEX:

TOPHAT_VERSION:

TOPHAT_OPTIONS:

BOWTIE_VERSION:

SAMTOOLS_VERSION:

Cufflinks

omics_pipe.modules.cufflinks.cufflinks(sample, cufflinks_flag)

Runs cufflinks to assemble .bam files from TopHat.

input:

accepted_hits.bam

output:

transcripts.gtf

citation:

Trapnell C, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology doi:10.1038/nbt.1621

link:

http://cufflinks.cbcb.umd.edu/

parameters from parameters file:

TOPHAT_RESULTS:

CUFFLINKS_RESULTS:

REF_GENES:

GENOME:

CUFFLINKS_OPTIONS:

CUFFLINKS_VERSION:

Cuffmerge

omics_pipe.modules.cuffmerge.cuffmerge(step, cuffmerge_flag)

Runs cuffmerge to merge .gtf files from Cufflinks.

input:

assembly_GTF_list.txt

output:

merged.gtf

citation:

Trapnell C, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology doi:10.1038/nbt.1621

link:

http://cufflinks.cbcb.umd.edu/

parameters from parameters file:

CUFFMERGE_RESULTS:

REF_GENES:

GENOME:

CUFFMERGE_OPTIONS:

CUFFLINKS_VERSION:

Cuffmergetocompare

omics_pipe.modules.cuffmergetocompare.cuffmergetocompare(step, cuffmergetocompare_flag)

Runs cuffcompare to annotate merged .gtf files from Cufflinks.

input:

assembly_GTF_list.txt

output:

merged.gtf

citation:

Trapnell C, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology doi:10.1038/nbt.1621

link:

http://cufflinks.cbcb.umd.edu/

parameters from parameters file:

CUFFMERGE_RESULTS:

REF_GENES:

GENOME:

CUFFMERGETOCOMPARE_OPTIONS:

CUFFLINKS_VERSION:

Cuffdiff

omics_pipe.modules.cuffdiff.cuffdiff(step, cuffdiff_flag)

Runs Cuffdiff to perform differential expression. Runs after Cufflinks. Part of Tuxedo Suite.

input:

.bam files

output:

differential expression results

citation:

Trapnell C, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology doi:10.1038/nbt.1621

link:

http://cufflinks.cbcb.umd.edu/

parameters from parameters file:

CUFFDIFF_RESULTS:

GENOME:

CUFFDIFF_OPTIONS:

CUFFMERGE_RESULTS:

CUFFDIFF_INPUT_LIST_COND1:

CUFFDIFF_INPUT_LIST_COND2:

CUFFLINKS_VERSION:

R Summary Report

omics_pipe.modules.RNAseq_report_tuxedo.RNAseq_report_tuxedo(sample, RNAseq_report_tuxedo_flag)

Runs R script with knitr to produce report from RNAseq pipeline.

input:

results from other steps in RNAseq pipelines

output:

html report

citation:

20. Meissner

parameters from parameter file:

WORKING_DIR:

R_VERSION:

REPORT_RESULTS:

DPS_VERSION:

PARAMS_FILE: