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Question: Downloads Maf Files
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gravatar for Navin Rustagi
5.7 years ago by
Navin Rustagi • 10
Navin Rustagi • 10 wrote:
Hi, I want to download MAF files for the exonic regions of the genome. Additionally I want the sequences to be in phase as well. How does one do that. Regards, Navin
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modified 5.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.7 years ago by Navin Rustagi • 10
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gravatar for Jennifer Hillman Jackson
5.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Navin, This recent post has much related information in it, including publication links that you will likely find helpful: http://lists.bx.psu.edu/pipermail/galaxy-user/2013-March/005997.html For your purposes, UCSC has "exons datasets" available directly for certain genomes. These are .fasta data extracted from MAF alignments. I don't know if these are useful for not for your purposes, but hg19 is one of them and this is the location: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/alignments/ To extract MAF data, the general path would be to: 1. load MAF data into your history as a dataset (local or public Main server) or have pre-cashed MAF data in a local 2. obtain exon coordinates as a dataset in history 3. use the tool " Fetch Alignments -> Stitch Gene blocks given a set of coding exon intervals" 4. download result, for large file, using wget or curl in a terminal prompt can speed things up Hopefully this helps, please let us know if you need more assistance, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
ADD COMMENT • link written 5.7 years ago by Jennifer Hillman Jackson ♦ 25k
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