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Question: Missing genome for SAM-to-BAM conversion
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gravatar for nicholas.anthony
2.2 years ago by
nicholas.anthony • 0
nicholas.anthony • 0 wrote:

Hi,

I have a SAM file of aligned RNA-Seq reads that I need to convert to a BAM. Problem is, when I try to use SAM-to-BAM conversion, there aren't any genomes listed in the dropdown, and I'm having trouble finding the mouse mm9 genome in a format that Galaxy understands. I feel like the mouse mm9 genome should already be available on Galaxy. Is there a way to find and upload it so that I can shrink this unwieldy file?

Thanks,

Nick
input tool metadata database samtools • 641 views
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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by nicholas.anthony • 0
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gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Assuming that you are working at http://usegalaxy.org, assign the "database" for the dataset to be "mm9" and the same genome will appear in the drop-down menu on the form. https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

Thanks! Jen, Galaxy team
ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k
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