Hello, Yes, you are correct, the expanded BED format or genePred format is required if you want to use the Custom track/Table browser method. Here are some links that can help.
http://genome.ucsc.edu/FAQ/FAQformat http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Sequence ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Chris Oldmeadow" <[email protected]> wrote: > From: "Chris Oldmeadow" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Sent: Monday, August 31, 2009 5:50:27 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] protein sequence from custom file > > Hi again, > > Does my custom track need to be identifiable as codon? eg I currently > just have chrom chromstart and chrom end - do I need to include > thickstart > and thickend for the browser to identify the sequence as being coding > for it to give me the option to output mRNA sequence? > > Cheers, > Chris > > > On Mon, Aug 31, 2009 at 08:51:51AM -0700, Jennifer Jackson wrote: > > Hello, > > Iif you have the coding (no URT, not intron) mRNA, then use the > protein translation tool. > > Home page -> Utilities -> > http://www.soe.ucsc.edu/~kent/dnaDust/dnadust.html > > > > mRrna sequence for custom tracks can be directly obtained from the > Table browser. Set the primary track as the custom track and output as > sequence. > > > > Thanks, > > Jennifer Jackson > > > > > > ------------------------------------------------ > > Jennifer Jackson > > UCSC Genome Bioinformatics Group > > > > ----- "Chris Oldmeadow" <[email protected]> wrote: > > > > > From: "Chris Oldmeadow" <[email protected]> > > > To: [email protected] > > > Sent: Sunday, August 30, 2009 8:30:29 PM GMT -08:00 US/Canada > Pacific > > > Subject: [Genome] protein sequence from custom file > > > > > > Hi, > > > > > > Is it possible to extract protein sequence from just the > positions > > > from a custom track? I know it is possible to obtain the protein > > > sequence using the group "gene and gene prediction". When I try > to > > > create an intersection with my custom track (which are > coordinates > > > within exons) I can only obtain the protein sequence for the > whole > > > genes that intersect with my positions. What Id like are just the > > > protein sequences corresponding to the positions only. Is this > > > possible using the table browser? if not is there another tool > which > > > can do this? > > > > > > Best, > > > Chris > > > > > > > > > _______________________________________________ > > > Genome maillist - [email protected] > > > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
