Hi Bibek, For information about step (and PhastCons files in general), see http://genome.ucsc.edu/goldenPath/help/phastCons.html. Also, on that page is this information about gaps, "A new declaration line is inserted in the file when the /chrom/ value changes, when a gap is encountered (requiring a new /start/ value), or when the /step/ interval changes." There are a many reasons why there are gaps, one being that where there is no conservation, there is no score (this is the nature of the HMM models that are making these numbers).
For calculating the conservation score for a small region, you can use the mean. See this previously answered question for more information: https://lists.soe.ucsc.edu/pipermail/genome/2009-July/019616.html For your last question, the easiest way to do this is using our Table Browser tool. Click on "Tables" on the blue bar on the top of the main page. In the Table Browser, select mm9 as well as the track and table you are using (Conservation; phastCons30way), and then create an intersection with the genes track of your choice (click "create" next to "intersection:"). For more information about using the Table Browser see "Using the Table Browser" by scrolling down past the Table Browser form or the "User's Guide" at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. For specific information about creating intersections, see http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Bibek wrote, On 11/05/10 07:01: > Hi, > I downloaded phastcons score of mouse (mm9) through FTP > (hgdownload.cse.ucsc.edu) from > /goldenPath/mm9/phastCons30way/vertebrate. I checked file, chr1.data & > found that first block starts at 3000306, whereas next block starts at > 3002512. See below- > fixedStep chrom=chr1 start=3000306 step=1 > fixedStep chrom=chr1 start=3002512 step=1 > > I believe each line on this file represents each position of chromosome, > being step=1. Please clarify if i am wrong. > > The difference between beginning of above 2 blocks is 2207, but i found > only 2175 lines for phastcons score. This indicate that phastcons scores > of few bases (about 32) are not given in the file. Does it mean 32 > nucleotides before start of next block (i.e. 3002512) do not show > alignment & thus no score. Please clarify. > > Another query, If i wish to calculate conservation score of a stretch of > 7-8 nucleotides, what should i adopt. > > Lastly, if i wish to convert chromosomal coordinates of these files into > positions within the gene, which method or track file of mm9 should i use. > > Thank you in advance. > > regards, > Bibek > > > > > IMPORTANT NOTICE: This e-mail and any attachments may contain > confidential or sensitive information which is, or may be, legally > privileged or otherwise protected by law from further disclosure. It > is intended only for the addressee. If you received this in error or > from someone who was not authorized to send it to you, please do not > distribute, copy or use it or any attachments. Please notify the > sender immediately by reply e-mail and delete this from your > system. Thank you for your cooperation. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
