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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