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
