Hi, Mitja, You can download BLAT and run it on the commandline.
You might have to compile it yourself if it's not available for your platform, but it's not too hard. BLAT is free for non-commercial use. -Galt 7/22/2011 4:07 AM, Mitja Mitrovic: > Dear UCSC team, > > below i provide my previous question and the answer from your colleague to > avoid > confusion in future. So once more, how can I make a custom track from fasta > file > containing cca. 100.000 sequences? Blat allows only 25 per time. Maybe you > have > scripts for that? > > Thanks, > > Mitja > > > > Hi Mitja, > > You will want to use Blat to map your fasta sequence to the genome and > then generate the output PSL format. The PSL format can the be > uploaded as a custom track. > > To do this click on "Blat" from the blue navigation bar. Select the > appropriate Genome,Assembly,Query type, Sort output, and select "PSL" > for the Output type. > > Once you have the PSL formatted output you can upload your custom > track by going to the gateway page > (http://genome.ucsc.edu/cgi-bin/hgGateway) and clicking on "custom > tracks". > > If you have further questions, please contact the mailing list: > [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > > ---------- Forwarded message ---------- > From: Mitja Mitrovic<[email protected]> > Date: Thu, Jul 21, 2011 at 9:16 AM > Subject: [Genome] New ncRNA track > To: [email protected] > > > Dear UCSC team, > > I have a fasta file of approx. 100.000 sequences (up to 50 bp in length). I > would like to create a custom track with those sequences to see where they > fall > in the genome. Therefore I would need a ped file with bp position ect. So, my > question is how can i make a custom track from this fasta file? Thanks in > advance! > > Mitja > ******************************************************** > Mitja Mitrovic > PhD Student > Department of Genetics > Oostersingel, Ingang 47 > 9713 EX Groningen > The Netherlands > 2nd floor, room E2.047 > Phone:+31(0)50-3617-105 > 53°15'N 06°35'E > ******************************************************** > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
