Hello Hiram, I was not aware of this Genomewiki site. So if I understand correctly, I must use hgWiggle command to retrieve the data, and this command is part of genome browser software that I first must install on linux/unix with some additional databses. I was more interested in specific external script (preferably something that works on windows) that can deal with wiggle+wib independently.
Thanks, Avi ________________________________ From: Hiram Clawson <[email protected]> To: Tatamil Tatamil <[email protected]> Cc: [email protected] Sent: Thursday, December 25, 2008 4:12:17 AM Subject: Re: [Genome] phyloP28wayPlacMammal Good Evening Avi: These tables you are referring to are the "wiggle" types of tables. Yes, you will need the .wib files locally to process this this data, as well as the .txt.gz dumps of the SQL table. See also: ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/multiz28way ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format http://genomewiki.ucsc.edu/index.php/Wiggle --Hiram Tatamil Tatamil wrote: > Hello to the UCSC staff and all other readers, > > I am working on cooperative genomics computer program that requires analyzing > conservation of introns genome-wide. As far as I understand the > phyloP28wayPlacMammal, phastcons17way (and similar tables) are designed for > such purposes. It would be realy nice if you can help in resolve some > mysteries about these tables: > > > 1) I see that the table directs me to a file named *.wib. and I'm wondering > if it is nessasery to use this file, or that the table itself can be usefull > enough for geting accurate information the sections it reports about ? > > 2) Is there any simple way to rapidly get to the exact position of *.wib in > windows ? > > 3) what sumSquares, sumData, validCount mean? > 4) I see that sometimes the phastcons17way table referes to gapped regions as > highly conserved, is there a way to avoid this false informations, and does > phyloP28wayPlacMammal suffer from the same problem ? > > 5) I understand that each raw represent about 1025 nucleotides but that > sometimes the number of rows is samller, why ? what does it mean ? > > Many thanks, Avi > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
