UAB Galaxy RNA Seq Step by Step Tutorial

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Attention: Research Computing Documentation has Moved

Please use the new documentation url for all Research Computing documentation needs.

As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

Galaxy RNA-Seq Step-by-Step Tutorial/Protocol

Upload data

* specify organism (request or include fasta if not in list)
* QC check

Align using TopHat

QC alignment

* %mapped
* visualize in IGV or IGB

Construct transcripts : Cufflinks

* Denovo vs existing annotation
* UAB Modified Reference annotations

Compare transcript levels: cuffdiff/cuffcompare