Question: Use whole genome or cDNA sequences for RNAseq alignment
gravatar for dietahanson
3.4 years ago by
dietahanson0 wrote:


  I'm working on my first RNAseq analysis, and I'm unsure of how to proceed with my TopHat2 alignment.  In all the documentation for TopHat2, reference is made to aligning to a genome (which I interpret as "whole genome sequence"), but wouldn't it be faster to align only to the cDNA sequences?  I have both for my organism (Gasterosteus aculeatus) and plan to use TopHat2 in Galaxy.

Thanks for any suggestions,


rna-seq cdna alignment tophat • 1.7k views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by dietahanson0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


There are many sources that describe the difference between transcriptome and genome RNA-seq analysis, but this course from UC Davis is a great start:

If you choose another source, most if not all of the options for this tool set (if given with line-command usage) can be also used with the Galaxy wrapped version of the tool. 

For general help with getting started with Galaxy, please see our wiki. The Support page lists the important resources at the very top:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k
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