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Question: SnpEff (Galaxy) troubleshoot
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gravatar for sanjay
16 months ago by
sanjay • 0
sanjay • 0 wrote:

I have got Mpileup data. I wish to further understand SNP effect using snpeff. Unfortunately, in Galaxy when i select reference genome from history i am required to fill "Additional annotations" and "Non-coding and regulatory annotation". I wonder if anyone can guide me through this.

My reference sequence is Mycobacterium tuberculosis"H37Rv" in fasta format and i am working with illumina whole genome sequence data.

I am using galaxy for the first time.
snpeff snp • 417 views
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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by sanjay • 0
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gravatar for Jennifer Hillman Jackson
16 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This tool only has pre-computed indexes loaded at Galaxy Main (http://usegalaxy.org) for a few genomes. Yours is not one of them.

Check with the other related SnpEff tools to see if your genome has indexes available. If so, download and use.

Please be aware that there are some known issues with this functionality. The ticket here explains the problem and current workaround options. https://github.com/galaxyproject/galaxy/issues/3969

Thanks, Jen, Galaxy team
ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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