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,

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