Question: Addding iGenomes inGalaxy
0
gravatar for Vijay Kumar
2.6 years ago by
Vijay Kumar20
Vijay Kumar20 wrote:

If i download iGenome of particular species (In may case Chicken) from http://ccb.jhu.edu/software/tophat/igenomes.shtml, after uploading into Galaxy, i can use this genome indexes for my reference genome instead of going to build custom genome reference.

rna-seq • 582 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Vijay Kumar20
1
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Yes, the content here has both the reference annotation (gtf) and the reference genome (fasta). The fasta can be used as a custom genome. If the target is galGal3, this reference genome is already indexed for HISAT2, so just the gtf would be needed. Also indexed for HISAT2 is galGal4, but I do not believe there is a gtf from iGenomes yet for this build.

Just please be aware the galGal3/galGal4 are not indexed for Tophat (aka Tophat2) and BWA/BWA-MEM for technical reasons that are yet unresolved. These two would probably fail for memory if used as a custom genome at http://usegalaxy.org. The other genome sources may or may not work. If you try any of these and the job fails for memory, then moving to a local or cloud Galaxy with a compute-intensive level of dedicated resource would be the solution (over 64 GB job memory).

Best, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
0
gravatar for Vijay Kumar
2.6 years ago by
Vijay Kumar20
Vijay Kumar20 wrote:

Dear Jenni, Thank you for your kind support.

ADD COMMENTlink written 2.6 years ago by Vijay Kumar20
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