Hi Ann, Here are the step-by-step instructions to retrieve data from the Table Browser.
1. Click here: http://genome.ucsc.edu/cgi-bin/hgTables 2. For REPEAT MASKER, make the following selections: clade: Mammal genome: Mouse assembly: July 2007 (NCBI37/mm9) group: Variation and Repeats track: RepeatMasker table: rmsk region: genome (or select "position" and enter your location of interest) output format: all fields from selected table output file: enter a file name file type returned: plain text 3. Click "get output". 4. For SIMPLE REPEATS, make the following selections: clade: Mammal genome: Mouse assembly: July 2007 (NCBI37/mm9) group: Variation and Repeats track: Simple Repeats table: simpleRepeat region: genome (or select "position" and enter your location of interest) output format: all fields from selected table output file: enter a file name file type returned: plain text 5. Click "get output". For more information on how to use the Table Browser, please see: http://genome.ucsc.edu/cgi-bin/hgTables#Help. Please contact us again at [email protected] if you have any further questions. Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 9/16/2011 7:12 PM, Ann Eileen Miller Baker wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
