UAB Galaxy RNA Seq Step by Step Tutorial

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Contents

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

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