RNA-seq pipeline for the GTEx Consortium
Name
RNA-seq pipeline for the GTEx Consortium
Description
This repository contains all components of the RNA-seq pipeline used by the GTEx Consortium, including alignment, expression quantification, and quality control.
Source URL
Aliases
kyle-gaulton:workflow_RNAseqPipelineForGTExConsortium
Workflow Repositories
Submitter Comment
The GTEx RNA-seq pipeline is provided as a Docker image.
Analysis Steps
6 items
Aliases
Input Content Types
Output Content Types
RNAseq GTEx pipeline BAM to FASTQ conversion step
bam-to-fastq-conversion-step
- kyle-gaulton:workflow_RNAseqPipelineForGTExConsortium_step1_BamToFastq
alignments
reads
RNAseq GTEx pipeline bamsync optional step
bamsync-optional-step
- kyle-gaulton:workflow_RNAseqPipelineForGTExConsortium_step3_syncBAMs
alignments
alignments
RNAseq GTEx pipeline Picard mark duplicates step
picard-mark-duplicates-step
- kyle-gaulton:workflow_RNAseqPipelineForGTExConsortium_step4_PicardMarkDuplicates
alignments
alignments
RNAseq GTEx pipeline quality control step
rnaseqc-quality-control-step
- kyle-gaulton:workflow_RNAseqPipelineForGTExConsortium_step5_RNA-SeQC
alignments
sparse gene count matrix, sparse transcript count matrix
RNAseq GTEx pipeline RSEM transcript quantification step
rsemtranscript-quantification-step
- kyle-gaulton:workflow_RNAseqPipelineForGTExConsortium_step6_RSEM
alignments, sparse gene count matrix, sparse transcript count matrix, transcriptome alignments
signal
RNAseq GTEx pipeline STAR alignment step
star-alignment-step
- kyle-gaulton:workflow_RNAseqPipelineForGTExConsortium_step2_STAR
reads
alignments, sparse gene count matrix, sparse transcript count matrix, transcriptome alignments
Attribution
Award
Supported by National Institutes of Health (NIH) grants U24 DK138515, U24 DK138512
Supplemental funds from the NIH Office of Data Science Strategies
Supplemental funds from the NIH Office of Data Science Strategies