Identifier: WF_254045.d5


This repository contains all components of the RNA-seq pipeline used by the GTEx Consortium, including alignment, expression quantification, and quality control. SamToFastq: BAM to FASTQ conversion STAR: spliced alignment of RNA sequence reads (v2.5.3a) Picard MarkDuplicates: mark duplicate reads RSEM transcript expression quantification (v1.3.0) bamsync: utility for transferring QC flags from the input BAM and for re-generating read group IDs RNA-SeQC: QC metrics and gene-level expression quantification (v1.1.9) Reference indexes for STAR and RSEM are needed to run the pipeline. All reference files are available at gs://gtex-resources. GTEx releases from V8 onward are based on the GRCh38/hg38 reference genome. Please see [TOPMed_RNAseq_pipeline]( for details and links for this reference. Releases up to V7 were based on the GRCh37/hg19 reference genome (download). For hg19-based analyses, the GENCODE annotation should be patched to use Ensembl chromosome names: zcat gencode.v19.annotation.gtf.gz | \ sed 's/chrM/chrMT/;s/chr//' > gencode.v19.annotation.patched_contigs.gtf A 2x76 bp paired-end sequencing protocol, will use a sjdbOverhang of 75



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