Hello Alyaa, This depends on what kind of summary you are trying to obtain. The Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) has built in functionality for generating summary statistics. Once in the Table Browser select your assembly of interest and:
group: Variation and Repeats track: RepeatMasker table: rmsk then click on the "summary/statistics" button at the bottom to get info for the whole table. If you are trying to come up with a count of each item type using the Table Browser you could filter for that item type and then use the "summary/statistics" button to get the item count and statistics. For example: filter: (click "create") then repClass 'does' match ' LINE' (you could also filter based on repFamily) and hit submit then "summary/statistics" to get the "item count". If you are comfortable working with the command line and mysql you could use remote mysql access to our data to run a query similar to: select repClass,count(*) from rmsk group by repClass; which would return the item counts for all the repeat classes. For more info on remote mysql access see this FAQ: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 6/13/12 12:18 AM, Alyaa Mahmoud wrote: > Hi All > > I have a question with regards to the output of repeat masker. I downloaded > the chromOut.tar.gz from the UCSC browser and I would like to summarize > the output by grouping repeats into families (LINES, SINES, DNA, LTR > ...etc). How is this possible ?? > > Thanks a lot > Alyaa _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
