Hi Rocky, To download data from the UCSC genome browser, the easiest tool is to use the genome browser which can be accessed by clicking on the "Tables" link from the blue navigation bar.
To get all of the miRNA regions using TargetScan the track you want to use is TS miRNA sites. You didn't indicate which assembly you would like to extract the data from. The latest assemblies, such as mm9 and hg19, use TargetScan 5.1. Once you get there set the following clade, genome, and assembly to what you are interested in. Then set the following: group: Genes and Gene Prediction Tracks track: TS miRNA sites table: targetScanS region: genome output format: all fields from primary and related tables output file: FileName (this is if you want to save it) click "get output" For PITA, you might want to take a look at these custom tracks from this lab: http://genie.weizmann.ac.il/pubs/mir07/mir07_browse.html Please keep in mind that if you have any questions about these tracks you will need to contact the lab that created these tracks. You can download the custom track data by first viewing the custom track in the browser and then by clicking on "Tables". Then set the following: group: Custom Tracks track: Select the one that you want table: Select the one that you want region: genome output format: all fields from primary and related tables output file: FileName (this is if you want to save it) click "get output" I hope this helps. If you have further questions, please email the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: 하오잠 로 <[email protected]> Date: 2011/6/22 Subject: [Genome] [Rocky] - TargetScan v4.1 and PITA in UCSC genome browser To: [email protected] Cc: [email protected], [email protected] Dear Madam, Could you please tell me how to download the miRNA target seed-matching regions predicted by TargetScan v4.1 and PITA from UCSC genome browser. I would be glad for your support and cooperation. I am eagerly waiting for your mail. Warm regards, Rocky _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
