https://github.com/mlin/rseqc

RNA-Seq Quality Control: Generates QC metrics for RNA-Seq data using the RSeQC suite; a graphical report of these metrics can be viewed on the DNAnexus website
https://github.com/mlin/rseqc

Last synced: about 1 year ago
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RNA-Seq Quality Control: Generates QC metrics for RNA-Seq data using the RSeQC suite; a graphical report of these metrics can be viewed on the DNAnexus website

• Host: GitHub
• URL: https://github.com/mlin/rseqc
• Owner: mlin
• License: gpl-3.0
• Created: 2013-09-18T04:17:43.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2013-09-18T05:56:56.000Z (over 12 years ago)
• Last Synced: 2025-04-03T10:37:51.395Z (about 1 year ago)
• Language: C
• Homepage: https://platform.dnanexus.com/app/rseqc
• Size: 2.04 MB
• Stars: 0
• Watchers: 1
• Forks: 10
• Open Issues: 0
• Metadata Files:
  • Readme: Readme.md
  • License: COPYING

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README

          
This app implements selected packages from the [RSeQC

suite](http://code.google.com/p/rseqc/wiki/Manual). These are:

* geneBody_coverage

* inner_distance

* junction_annotation

* read_distribution

* read_duplication

The app requires as input RNA-Seq mappings and a BED file describing the

gene model used for or derived from these mappings.

Optionally, the user may estimate the amounts of different contaminants in

the sample. This is done by suppling sequences through the "contaminants"

input, which takes any number of [ContigSet

objects](http://wiki.dnanexus.com/Types/ContigSet). FASTA files may be

imported into ContigSet objects using the **Genome Importer** app.

One or more [Reads objects](http://wiki.dnanexus.com/Types/Reads) MUST also

be given if contaminants are given. The reads will be matched against each

contaminant using the BWA app and the percent mapping will be stored.

The output is a set of charts in a report that can be viewed by selecting

the report object in the data browser.