Question: dm6 multiz MAF gives smaller than expected
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nicanicagm • 0 wrote:
Hi,
Maybe a basic question.
I am trying to get the homolog aligned sequences for a huge gene in drosophila (Sls). It spans 75kb, located chr3L:2039681-2115611. I tried to get a MAF file from UCSC table browser, and sent it to galaxy. Then I used the "Join MAF blocks by Species" command to merge the MAf blocks into 27 species. Finally I converted the MAF file to fasta (MAF to Fast command). Everything worked ok except the final fasta alignment file spans a 16kb region instead of 75kb. At some point during the process some regions are being deleted and I don't understand why.
best
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modified 2.7 years ago
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Jennifer Hillman Jackson ♦ 25k
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2.7 years ago by
nicanicagm • 0
