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
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
On 3/28/13 8:22 AM, Navin Rustagi 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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