Question: Downloads Maf Files
gravatar for Navin Rustagi
5.7 years ago by
Navin Rustagi10 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
ADD COMMENTlink modified 5.7 years ago by Jennifer Hillman Jackson25k • written 5.7 years ago by Navin Rustagi10
gravatar for Jennifer Hillman Jackson
5.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Navin, This recent post has much related information in it, including publication links that you will likely find helpful: 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: 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
ADD COMMENTlink written 5.7 years ago by Jennifer Hillman Jackson25k
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