Hello Nipun, An alternative to entering each data point in manually is for you to create a custom track here: http://genome.ucsc.edu/cgi-bin/hgCustom
You can find more information on creating a custom track here: http://genome.ucsc.edu/goldenPath/help/customTrack.html and our file types here: http://genome.ucsc.edu/FAQ/FAQformat.html Once you have created a custom track, you can use our Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables and create an intersection with whichever track on the Genome Browser you are interested in. If you have two tracks - A and B - an intersection will produce output with all lines of file A that overlap with file B. http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection Should you want to do a merge between the two tracks/tables, then send both over to Galaxy (use the Table browser and check output "Galaxy") and perform an interval intersection. This will produce output with all lines of file A along with the lines from file B that have overlap. I hope this is what you need. Please feel free to contact us again if you have further questions. Antonio Coelho UCSC Genome Informatics Group nipun kakkar wrote: > I was trying to figure out a way to predict an amino acid call for all the > transcripts for a given position in the genome. > > for e.g. if i have a file with records like: > > chr1 103260930 + A > > where + is the strand > A is the allele seen at that loci. > > I would like to find out all the transcripts covering this position and > the > amino acid this loci belongs to. > > I understand that this is what UCSC genome browser is doing essentially, but > i wanted to run a file with 1000 records and therefore it won't be feasable > to manually enter the data in UCSC. > > Is there a set of files someone can point me to so that i can compute this? > Or if there any other suggestions from the group? > > Thanks, > Nipun > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
