You can use the table browser to search your custom track for your names. Use the "filter" function. You can also find out how your GFF file is translated into a bed file. Your input GFF file is turned into a bed file within the browser. There may be complication with the name chosen for your item since GFF files can vary quite a bit in their definition of what is the name of items. In your example, your names do survive the transition, but this is not necessarily always the case.
--Hiram ----- Original Message ----- From: "Minh Bui" <[email protected]> To: "Brooke Rhead" <[email protected]> Cc: [email protected] Sent: Wednesday, August 18, 2010 3:24:46 PM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] Search on custom track? HI Brooke, Thank you for your response. Hopefully, this feature will be added to UCSC Genome Browser soon. Minh Bui. On Wed, Aug 18, 2010 at 6:10 PM, Brooke Rhead <[email protected]> wrote: > Hi Minh, > > I'm sorry, but there is currently not a way to make custom track contents > searchable in the in the Genome Browser. > > For future reference, either of these two pages are a good way to search > the mailing lists: > > > http://genome.ucsc.edu/FAQ/ > http://genome.ucsc.edu/contacts.html > > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 08/18/10 14:46, Minh Bui wrote: > >> Hi everyone, >> >> I am new to Genome Browse. I am sorry if this question is already asked >> somewhere. I dont know how to search in the mailing list. >> >> I just uploaded a GFF file: >> >> *browser position chr1:100856178-100856388* >> *track name=unactivated description="Unactivated HIV"* >> *chr1** **gmapper** **unactivated** **100856178** **100856388** **.** >> **-** >> **.** **GIQPZ7U01BCT25-S3_10_23* >> *chr1** **gmapper** **unactivated** **100856178** **100856390** **.** >> **-** >> **.** **GIQPZ7U01BFRU0-S3_10_23* >> *chr1** **gmapper** **unactivated** **100856178** **100856390** **.** >> **-** >> **.** **GIQPZ7U01BM9JU-S3_10_23* >> >> >> Is there anyway that I can search on custom track using the last column >> such >> as *GIQPZ7U01BCT25* OR **S3_10_23* or *GIQPZ7U01BCT25-S3_10_23* ? >> How can I adjust my GFF to perform this search (GIQPZ7U01BCT25-S3_10_23 is >> a >> read's name) >> Thank you very much, >> Minh Bui. >> _______________________________________________ >> 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
