Hi Jian, A bit more about splitting + and - strand items from one BAM file into two custom tracks... firstly, the default BAM coloring mode uses different colors for the two strands, and sorts items by strand before by position, so if you haven't already given it a try, a single BAM custom track might be adequate for visually distinguishing + vs -.
If not, then you will need to split your BAM file into two BAM files in order to make two custom tracks. You can do this with samtools (samtools.sourceforge.net) like this: samtools view -b -h -f 0x10 my.bam > my.reverse.bam samtools view -b -h -F 0x10 my.bam > my.forward.bam (then samtools index the new bam files) The first command uses "-f 0x10" which means "include an item only if the bit for reverse (16 = 0x10) is set in the flag field". The second command uses "-F 0x10" which excludes items with that bit. Try "samtools --help" for more detailed description of options. For help with downloading, installing or using samtools, there is [email protected] . Hope that helps, Angie ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Yuan Jian" <[email protected]> > Cc: [email protected] > Sent: Monday, August 16, 2010 12:38:18 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] custom track for bam file > > Hello Jian, > > Creating/loading two tracks is certainly possible. Load each one > following the BAM custom track instructions here: > http://genome.ucsc.edu/goldenPath/help/bam.html > > If you would like more assistance, please feel free to contact the > mailing list support team again. > > Regards, > > Jen > UCSC Genome Browser Support > > On 8/16/10 5:21 AM, Yuan Jian wrote: > > Hi good UCSC genome people, > > > > I have generated a BAM file. now I try to make custom tracks for the BAM > > file. > > > > my question is > > can I put + strand and - strand in two different custom tracks? and how to > > do? > > > > thanks > > jian > > > > > > > > > > > > > > _______________________________________________ > > 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
