Hi Adriane, Here is an even better way to get the output that you want:
>From the table browser: http://genome.ucsc.edu/cgi-bin/hgTables 1) Set the assembly to: Hg18 2) Set group to: gene and gene prediction tracks 3) Set track to: RefSeq genes 4) Make sure region is set to: genome 5) Set output format to: custom tracks 6) Click on get output 7) Select "3' UTR Exons" 8) Click on "Get custom track in table browser" Now that your RefSeq data is in a track we will need to intersect it with the miRNA data. This can be done by doing the following: 1) Set the track to: sno/miRNA 2) Click on "create" (next to intersection) 3) For group select: custom tracks 4) Set the track to the custom track you created 5) Click on "Submit" 6) Change output to: bed format 7) Click on "get output" 8) Select: Whole Gene 9) Click on "get Bed" Hope this helps. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Vanessa Kirkup Swing" <[email protected]> To: "Adrian Johnson" <[email protected]> Cc: [email protected] Sent: Thursday, May 13, 2010 3:00:39 PM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] miRNA target sites Dear Adrian, Please see this previously answered mailing list about retrieving miRNA data: https://lists.soe.ucsc.edu/pipermail/genome/2009-December/020695.html The track in the above response can be found in hg18. Please contact the mailing list again if you have further questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics ----- Original Message ----- From: "Adrian Johnson" <[email protected]> To: [email protected] Sent: Thursday, May 13, 2010 1:08:45 PM GMT -08:00 US/Canada Pacific Subject: [Genome] miRNA target sites Dear UCSC, How do I get a BED file of all the miRNA target sites located on 3'UTR of all human genes (RefSeq). For instance: chr1 11001 11026 miR218 chr1 11025 11051 miR281 thank you. Adrian _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
