Question: Reference genome in Galaxy cloud for RNA-seq
0
gravatar for nyegaard
2.9 years ago by
nyegaard0
European Union
nyegaard0 wrote:

Hi.

I am trying to align paired end reads from human samples using Tophat2 in Galaxy cloud.

Would you recommend to align to hg19 or hg38?

From where do I get such a reference genome?  I wonder if I need to download the entire file to my own computer and upload to cloud or is there an easier method?

 

Thank you for your help.

Mette

rna-seq tophat galaxy • 722 views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by nyegaard0
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Since this genome already exists in the default builds list for CloudMan, use this genome fetching Data Manager from the Tool Shed to install the genome. The source will be UCSC. 

If you use hg19, there is better reference annotation available for certain tools. In particular, the GTF from iGenomes can be used with the Tuxedo RNA-seq analysis tools (Tophat, Cuffdiff, etc). The iGenomes genes.gtf dataset contains all of the extra attributes that enable full functionality. 

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson25k
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