Hi Vinayak, The Table browser can do this for you. To get to the table browser click on "Tables" from the blue navigation bar which will take you to this page: http://genome.ucsc.edu/cgi-bin/hgTables.
Here is an example of the settings to use for hg19: clade: Mammal genome: Human assembly: hg19 group: Mapping and Sequencing Tracks track: Mapability table: wgEncodeCrgMapabilityAlign100mer region: genome (if the query is too large you will need to set this to position and do it chromosome by chromosome) filter: data value >= 0.5 and Limit data output to: 10,000,000 lines output format: bed format Click "get output" Repeat the above this for wgEncodeDukeMapabilityUniqueness35bp by changing the table to: table: wgEncodeDukeMapabilityUniqueness35bp If you are unfamiliar with the table browser, please see the following: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Vinayak Kulkarni <[email protected]> Date: Mon, Feb 27, 2012 at 6:00 PM Subject: [Genome] Analysis on specific regions of mappability track To: [email protected] Dear UCSC team, I am trying to analyze regions of the genome that have low mappability i.e mappability score 0.5 or higher. What would work best for me is a bed like file having just these regions in it (a plus would be having the score in the fourth column). I looked at the bigWig files in the downloads section (wgEncodeCrgMapabilityAlign100mer and wgEncodeDukeMapabilityUniqueness35bp) but could not figure out how to convert those into bed or a format where I could easily extract the relevant regions for a mappability score threshold (in my case 0.5 or higher). Could you please help me? Thanks a lot, Vinayak -- -- "Hesitating to act because the whole vision might not be achieved, or because others do not yet share it, is an attitude that only hinders progress"... Mahatma Gandhi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
