Hi Brooke, I did see this as an option, but it would be a big hassle due to the size of the data I'm working with. But thanks for passing it on! I really appreciate everyone's quick response time and suggestions.
Thanks! Jesse On Mon, Jul 25, 2011 at 1:03 PM, Brooke Rhead <[email protected]> wrote: > Hi Jesse, > > Your suggestions are being considered, but in the meantime, one of our > developers offered these comments: > > It's possible (though not convenient) to add an RGB tag to each line of BAM > to get per-item colors. See "Use R,G,B colors specified in user-defined tag" > in > http://genome.ucsc.edu/**goldenPath/help/**hgBamTrackHelp.html<http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.html>. > That would require some disk space and time depending on the size of the BAM > files, but it's conceptually simple: > > 1. convert BAM to SAM > 2. feed SAM to script that looks at the strand bit in the flag column and > appends YC:Z:<rgb triplet> tag > 3. convert modified SAM to BAM, index the new BAM > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > On 07/22/11 21:58, Jesse Rodriguez wrote: > >> Hi Katrina, >> >> Thanks for passing this along and for the info -- I saw the bam >> visualization options, but none of the combinations yielded any easy way >> to >> see both strand info and variants. >> >> Jesse >> >> On Fri, Jul 22, 2011 at 5:49 PM, Katrina Learned <[email protected] >> >wrote: >> >> Hi Jesse, >>> >>> Thank you for your feedback. I will pass this suggestion on to management >>> for consideration. >>> >>> You can change the coloring of the alignments from the track controls >>> page >>> of your track, which you can get to by right-clicking on the track and >>> selecting one of the configure options. Here is some information about >>> the >>> coloring options: >>> http://genome.ucsc.edu/****goldenPath/help/****hgBamTrackHelp.html<http://genome.ucsc.edu/**goldenPath/help/**hgBamTrackHelp.html> >>> <http://**genome.ucsc.edu/goldenPath/**help/hgBamTrackHelp.html<http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.html> >>> > >>> >>> >>> Please contact the mail list ([email protected]) again if you have any >>> further questions. >>> >>> Katrina Learned >>> UCSC Genome Bioinformatics Group >>> >>> Jesse Rodriguez wrote, On 07/22/11 12:56: >>> >>> Hello, >>>> >>>> Just as some feedback, I think the default forward/reverse coloring of >>>> the >>>> bam reads makes it very difficult to spot mismatches in the reads. This >>>> is >>>> made worse by the fact that the mismatches are only one pixel wide >>>> instead >>>> of being an entire base in width. It would be nice if the >>>> forward/reverse >>>> coloring could be customized at the very least since lighter colors >>>> would >>>> make the red of the mismatches stand out more, even if they weren't made >>>> 1 >>>> base wide. >>>> >>>> Jesse Rodriguez >>>> >>>> PhD Candidate >>>> Biomedical Informatics Program >>>> Stanford University >>>> ______________________________****_________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/****mailman/listinfo/genome<https://lists.soe.ucsc.edu/**mailman/listinfo/genome> >>>> <https:**//lists.soe.ucsc.edu/mailman/**listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>>> > >>>> >>>> ______________________________**_________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
