Title
RNA-seq of long RNAs (paired-end, stranded)
Assays
RNA-seq, siRNA knockdown followed by RNA-seq, shRNA knockdown followed by RNA-seq, CRISPR genome editing followed by RNA-seq, CRISPRi followed by RNA-seq
Description
ENCODE pipeline for paired-ended and stranded long RNA-seq data. 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 references used for this pipeline and exogenous RNA spike-in controls are described in the pipelines overview document.
Lab
ENCODE Processing Pipeline

Pipeline schematic

Documents

pipeline protocol
Description excerpt: Long RNA-seq pipeline: Includes overview, references, and spike-ins…
Description
Long RNA-seq pipeline: Includes overview, references, and spike-ins information about the pipeline
Submitted by
Kathrina Onate
Lab
J. Michael Cherry, Stanford