Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Reference genome in Galaxy cloud for RNA-seq
0
gravatar for nyegaard
3.2 years ago by
nyegaard • 0
European Union
nyegaard • 0 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 • 816 views
ADD COMMENT • link •
modified 3.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.2 years ago by nyegaard • 0
0
gravatar for Jennifer Hillman Jackson
3.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 3.2 years ago • written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 181 users visited in the last hour