Question: dm6 multiz MAF gives smaller than expected
gravatar for nicanicagm
2.7 years ago by
nicanicagm0 wrote:


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.


alignment multiz dm6 maf • 641 views
ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by nicanicagm0
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Loading MAF data from the UCSC Table browser will truncate the output (there is a data transfer limit of about 100k lines). Instead, load the data from the UCSC Downloads area.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.7 years ago by Jennifer Hillman Jackson25k
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