Hi Xianyao, I might have helped to make that file almost 3 years ago. I still have some local .bed files with names like TAMU_galGal3_customTrack.bed (Nov 7 2006) and TAMU_galGal3_all12.bed (Dec 1 2006). Unfortunately our mailing list server strips attachments so I did not see the file you sent. Can you please paste the first 5 lines of the file into email?
> I have some genes located in negative strand. I try to convert > them into positive strand. In general, we translate coordinates to the opposite strand by reversing the order of the coordinates, and subtracting each coordinate from the chromosome size. If you are taking gene coordinates from a custom track in the BED format, then the coordinates are already for the positive strand of the reference genome. If you are taking gene coordinates from some other source, please paste an example for one gene on the negative strand into email. I hope I understand your question correctly, but if not then please send any details that might help. Angie ----- "Xianyao Li" <[email protected]> wrote: > From: "Xianyao Li" <[email protected]> > To: [email protected] > Sent: Friday, September 18, 2009 1:13:54 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Question of chicken genome > > Hi, > > I use the file name as "TAMU Agilent custom track-Zhou" which was > built by your group too. > > I attached part of custom track. > > Please let me know if you need more information. > > Thanks > > Xianyao > > ________________________________ > > From: Xianyao Li > Sent: Thu 2009-9-17 PM 03:10 > To: [email protected] > Subject: Question of chicken genome > > > Hi, > > I sent my question and the answer given by Angie. Please post on the > list. > > Thanks, > > Xianyao > > ________________________________ > > From: Angie Hinrichs [mailto:[email protected]] > Sent: Thu 2009-9-17 PM 01:23 > To: Xianyao Li > Subject: Re: Question of chicken genome > > > Hi Xianyao, > > The answer depends on what file format your data is in, and which > genome assembly version you are using. > > Please send your question (including the above info) to > [email protected], our help list. Using the list helps to ensure > that your question is answered in a timely manner, it helps us to > track our efforts and to demonstrate our value to the community at > grant renewal time, and the searchable public archive of list > questions (available on the http://genome.ucsc.edu Contacts page) > helps all users to find answers to questions that have been asked > before. > > Thanks, > Angie > > > Dear Angie Hinrichs, > > This is Xianyao, from Texas A&M University. > > I have some genes located in negative strand. I try to convert > them into positive strand. > > Could you have some way to do it. > > Thanks > > Best regards, > > Xianyao > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
