RNA-seq Pipeline 2 (Single-ended, ENCODE)

  • Status: active
Title
RNA-seq Pipeline 2 (Single-ended, ENCODE)
Assays
RNA-seq
Description
Adopted pipeline for single-ended unstranded data long RNA-seq data as developed by the ENCODE RNA Working Group. RNA libraries generated from mRNAs (poly-A(+)), rRNA-depleted total RNA, or poly-A(-) populations that are size-selected to be longer than approximately 200 bp may be run through this pipeline. More information regarding uniform pipeline restrictions, references used for this pipeline, and exogenous RNA spike-in controls are described in the pipelines overview document.
Lab
AMP-T2D consortium
Award PI
T2D AMP Consortium
Pipeline Type
text_file
Pipeline Chain
/pipelines/DPL009OFN/
Pipeline Output
alignments, transcriptome alignments, signal, gene quantifications, transcript quantifications
Submitter comment
Adopted ENCODE single-ended RNA-seq pipeline (new version)

Pipeline schematic