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
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