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Question: Is it possible to group many MAF files?
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gravatar for mlwright
5 months ago by
mlwright • 30
mlwright • 30 wrote:

Hi,

I have an interval file with ~100 sequences from hg38 that I am trying to extract multiple alignments from. Currently, I have 25 MAF files (Chr 1-22, X, Y, M) from hg38 uploaded, but when I Stitch MAF Blocks for one of my MAF files, I get a bunch of empty alignments for stuff on other chromosomes. It seems like in order to get alignments, I have to pull out coordinates from each individual chromosome, Stitch MAF Blocks for each one, then piece everything together at the end.

I am wondering if it's possible to somehow group all my MAFs together so I can supply the interval file directly, with all chromosomes, like I would with the cached 100-way hg19 MAF file.

Thanks!
merge alignment cat text-mani maf • 176 views
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modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 5 months ago by mlwright • 30
1
gravatar for Jennifer Hillman Jackson
5 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, the MAFs can be stacked together into a single file. Try the tool Text Manipulation > Concatenate.

Please be aware that there are some new scaling issues with the MAF tools when very large custom MAFs are used. If you run into problems, please review the issue details, workarounds, and fix progress here: https://biostar.usegalaxy.org/p/28331/#28332.

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson ♦ 25k
1

Fantastic, thank you!

ADD REPLY • link written 5 months ago by mlwright • 30
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