Question: SnpEff (Galaxy) troubleshoot
gravatar for sanjay
9 months ago by
sanjay0 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 • 249 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson24k • written 9 months ago by sanjay0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson24k wrote:


This tool only has pre-computed indexes loaded at Galaxy Main ( 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.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson24k
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