Good Morning Kees-Jan: If you want to see just the numbers for each 150 base window, do not run the output of hgGcPercent through wigEncode. The purpose of wigEncode is to construct a pair of files to use in the genome browser to draw a graph of the data. The .wig file is loaded into the database. The .wib file is a compressed representation of the data values. If you want to extract the individual numbers for each 150 base window from the .wig/.wib files, use the command line tool: hgWiggle
See also: http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database http://genomewiki.ucsc.edu/index.php/Wiggle --Hiram ----- Original Message ----- From: "Kees-Jan Francoijs" <[email protected]> To: [email protected] Sent: Tuesday, March 29, 2011 5:10:32 AM Subject: [Genome] hgGcPercent problem Hi I have a problem running the hgGcPercent | wigEncode program(s). I noticed that the winsize is muliplied with 1024. I try to calculate the GC content for a 150 bp window line executed: hgGcPercent -wigOut -file=stdout -noDots -noLoad -win=150 yeast ./yeast.2bit | /home/hinri/bin/x86_64/wigEncode stdin yeast_gc150bp.wig yeast_gc150bp.wib yields the following wig file. chrI 0 153600 chrI.0 150 1024 0 gc150bp_mb05.wib 19.3 40.7 1024 40252.8 1.62621e+06 chrI 153600 230100 chrI.1 150 510 1024 gc150bp_mb05.wib 22.7 42 510 19980 805250 ... chrXVI 921600 948000 chrXVI.88 150 176 80857 gc150bp_mb05.wib 24 31.3 176 6692.1 261414 The interval is 153600 (which is 1024x150) instead of the requested 150 bp. Has somethings changed since i used it before without any problems. Regards Kees-Jan _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
