Hello Soofin,
To obtain "slices" of MAF alignments, send a custom track of the human
coordinates and the MAF alignment to Galaxy. Once there, use the function:
Fetch Alignments-> Extract MAF blocks
There are utilities in the kent source tree that will do this on the
line command, but the best one requires a local database. If you are
running a mirror, then the recommended utility would be "mafFrags".
Thanks,
Jen
---------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu/
On 2/10/10 1:32 PM, Soojin Yi wrote:
> Dear Genome,
>
> I have a file of positions in the hg18 that are of specific interest to me.
> I want to extract homologous sequences from the marmoset chain. For example,
> I want to extract marmoset chain sequences aligned to the chr1 995668-996276
> in hg18.
>
> I tried using the Table browser (using output format: sequence) but instead
> of a short (~600bps) sequence, it provides the whole contig
> (hg18_chainCalJac1_Contig4288 ). Is there any way I can extract only the
> sequences corresponding to the specified positions in the human genome?
>
> Many thanks in advance,
>
> Sincerely, Soojin Yi
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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