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Question: galGal5 reference genome and indexes
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gravatar for caroline.brossas
15 months ago by
caroline.brossas • 0
caroline.brossas • 0 wrote:

Hi I'm interested in the new Galgal 5 assembly obtained in dec2015, for the moment it is only possible to align reads against the Galgal4 assembly in Galaxy. Do you know when this new assembly (Galgal 5) will be available? Thanks a lot Caroline
assembly alignment genome indexes • 568 views
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modified 4 months ago by rasou2ba • 0 • written 15 months ago by caroline.brossas • 0
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gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I added the genome to the tracking list of databases to index. The lists are not complete - all of UCSC's genomes plus the NCBI/plant requests will be added during processing.

For now, obtain the genome from UCSC, load it to Galaxy, and use it as a custom reference genome.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

Hello,

I'm also interested in getting the Galgal5 assembly to find sequence motifs (similar to what's done in Galaxy's ChIP-seq tutorial). Has this assembly been added or will it be added anytime soon?

Thank you

ADD REPLY • link written 4 months ago by rasou2ba • 0

Hi Jen,

I'm looking in to transitioning my undergrad course chicken RNA-seq data analysis to Galaxy, however we need to have the updated galGal5 2015 genome assembly to do this. Do you have a time frame for adding this particular assembly?

Thanks!

ADD REPLY • link written 4 months ago by Ray_Enke • 0
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