ENCODE RNA-seq pipeline

Identifier: WF_0741dc.ac


This is the ENCODE-DCC RNA-sequencing pipeline. The scope of the pipeline is to align reads, generate signal tracks, and quantify genes and isoforms.

RNA-seq data is valuable as it allows the measure of RNA expression levels as a transcriptional readout and the study of RNA structures in order to understand how RNA-based mechanisms impact gene regulation and thus disease and phenotypic variation.

Job Costs*

Costs for this workflow typically vary between $10-$25 per job and depends mostly on the size and number of replicates.


Public example Job cost Notes
ENCSR954PZB total RNA-seq on human adrenal gland $11.25 This is a paired end sample with 2 replicates. Each of the 4 fastq files is around 4GB. Rerun of ENCODE experiment ENCSR954PZB
PVTT_RNA_seq $11.53 This is a paired end sample with 2 replicates.

*Job cost examples are for estimates only. To get a more accurate idea of job costs, try running a single job before running many jobs.

Code Repository
  • GitHub