Good Afternoon: Thanks for the problem report on the hgWiggle output. This was an old limitation of using data files instead of the database that can be removed the code. You will find this fixed in our next release of source code in about two weeks.
In the meantime, you can use the public MySQL server to perform this query correctly and more efficiently. Place the following three lines in a file in your home directory called .hg.conf db.host=genome-mysql.cse.ucsc.edu db.user=genomep db.password=password Set the permissions on the file: $ chmod 600 $HOME/.hg.conf Then, use the -db=mm9 argument with hgWiggle. The database access function will correctly show you the exact interval you specify. You do need to run the hgWiggle command while in the directory where your phastCons30way.wib file exists. It will need to read that file. There are not necessarily data values for all positions in the genome. The hgWiggle input will not give you values where data does not exist. Using a zero value for base positions that do not have data values could interfere with your statistics concerning the data values that do exist. Depending upon your experiment design, the zeros may have no effect. --Hiram liuxq wrote: > > Greetings, > I have two basic questions for phastcons. > > 1. Why some positions do not have phastcons values? How to treat these > positions? Is it ok to use zero for these positions? > > 2. When I use hgwiggle -doStats to extract phastcons value locally, I > find that the start and the end are different from what I supplied, following > is my command and the output. I use > -position=chr13:23654149-23654222 as the parameter for hgwiggle, but the > output display different values. What is the reason? > > li...@server $ ~/tools/hgwiggle/hgWiggle -position=chr13:23654149-23654222 > -doStats phastCons30way > # from file, Table: phastCons30way > # Chrom Data Data # Data Data Bases Minimum Maximum Range Mean > Variance Standard > # start end values span covered > deviation > chr13 23653329 23654352 1024 1 1024 0 1 > 1 0.580009 0.20296 0.450511 > > Thansk in advance and look forward to the reply. > > kindly regards, > Xiaoqiao Liu _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
