ENCODE RNA-seq pipeline

Version:
v1.2.1
Identifier: WF_0741dc.ac
Workflow
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Description

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.

Examples:

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.

Links
  • Encode Project Website

    https://www.encodeproject.org/rna-seq/

Code Repository
  • GitHub

    https://github.com/ENCODE-DCC/rna-seq-pipeline

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