Please use the twoBitToFa program to extract sequence from .2bit files. --Hiram
----- Original Message ----- From: "Peng Yu" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Tuesday, March 29, 2011 6:38:36 AM Subject: Re: [Genome] Perl Bio::Das download of repeatmasked sequences? Hi Hiram, I know that uscs browser source code should have a parer to this type of files (which is in C (according to the accompany header file), right?). Is there a library as simple as Bio::DAS that I can call from scripting language like perl or python without having to know the details of .2bit file format? http://www.perlmonks.org/?node_id=672251 Converting .2bit to fasta then using bioperl to parse fasta is one option. But it seems less straightforward. If there is a stand alone tool, it would be better. On Mon, Mar 28, 2011 at 7:33 PM, Hiram Clawson <[email protected]> wrote: > Please use the .2bit files fetched from hgdownload for > local access to genome sequence. > > --Hiram > > > On 3/28/11 9:19 AM, Peng Yu wrote: >> Hi, >> >> I'm wondering whether ucsc genome browser DAS has enabled the support >> repeatmasked sequences. I know that it was not available, but I want >> to double check if it is available now. >> >> https://lists.soe.ucsc.edu/pipermail/genome/2007-March/013165.html > -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
