16Sp11 Dear Genome Team, Thanks for the important start Katrina! I scanned all that Katrina suggested this evening and will go back to try out more parts that she suggested to reach my objective (contrasting the Dietrich DMIT usat loci with all usat loci in the mouse genome). Looking at ideas Katrina suggested (see below), my tentative conclusions and questions follow
(1) I feel the TRACK providing all mouse microsats will be REPEAT MASKER, which includes much more than microsats- I don't know if SIMPLE REPEAT will include all microsats- I suppose I will learn by comparing REPEAT MASKER with SIMPLE REPEAT tracks. (2) I would like to start inputting these two (REPEAT MASKER, SIMPLE REPEAT) into TABLE BROWSER and would appreciate knowing which parameters (the stream of filling in the blanks in the TABLE BROWSER ca. 15 steps) (3) Though the map is a valuable tool, for statistical analyses, I need the data output as text or excel tables, not as maps. Many thanks for helping me learn about all microsat loci in the mouse genome. Ann ---------- Forwarded message ---------- From: Katrina Learned <[email protected]> Date: Fri, Sep 16, 2011 at 5:09 PM Subject: Re: [Genome] finding microsatelllite loci in mouse genome To: Ann Eileen Miller Baker <[email protected]> Cc: [email protected] Hi Ann, We have several mouse tracks in the genome browser that provide data on the location of microsatellites. I think the first step is for you to read the track descriptions for these tracks and determine which you'd like to use to compare to the DMIT microsatellite data you already retrieved. I have provided the track names and links to their descriptions below. Microsatellite http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=microsat Simple Repeats http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=simpleRepeat RepeatMasker http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=rmsk It might be helpful to turn on the tracks and view them in the genome browser together to see how they compare. In fact, I have created a session for you in which I have turned on the tracks listed above as well as a custom track of all the DMIT microsatellites from the STS Marker track (this custom track is based on the directions we gave you for finding them originally) and the STS Marker track: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Katrina&hgS_otherUserSessionName=microsatellitesMm9 Once you have decided which track best fits your needs, you can write back to us via the mailing list ([email protected]) and we can assist you in retrieving the data via the Table Browser. Katrina Learned UCSC Genome Bioinformatics Group On 9/16/11 10:19 AM, Ann Eileen Miller Baker wrote: 16Sp11 Dear Genome team, 1. I expand my mouse DMIT microsatellite loci manuscript to include ALL MICROSATS (tandem repeats from 1 to 6 bp) that are different than those in Dietrich et al. 1996 NATURE database; i.e., my objective is determining if my results for Dietrich DMIT are a representative sample of all mouse microsats. 2. Can the UCSC team help me find these unknown microsats? If so, please list steps that I can easily follow (the more detailed the steps the fewer emails I will need to send the UCSC team); recall I used the TABLE BROWSER to find genomic elements occurring with DMIT loci earlier Many thanks, Ann _______________________________________________ Genome maillist - [email protected]https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
