Display replicate libraries with different colors

[ericguo]

Hi all,

I have two small RNA libraries that are biological replicates. I mapped the reads onto the genome using Bowtie and displayed the BAM files as two individual tracks on the UCSC genome browser. However, this is not very nice.

Ideally, I would like to color the reads from each library with a different color, so that I could display them in the SAME track. Because the two replicates are color labeled, I would be able to tell which experiment a particular read comes from.

I have two BAM files from each library. All I need to do is to label them with different colors, then merge them before displaying on genome browser.

Does anyone know how to do this?

Thanks in advance for your help!

-Eric

[droog_22]

Hi Eric,

You could use the some kind of user tag, e.g. YC:Z:247,251,255 in our BAM file. You can later tell the UCSC genome browser (or IGV) not to color the BAM track by the strand of the read (the default) but by your specific color tag.

You can read more about the SAM specifications here: http://samtools.sourceforge.net/SAM1.pdf or for color-coding your BAM tracks on UCSC here: http://altair.dartmouth.edu/ucsc/gol...TrackHelp.html

Cheers, Daniel

[swbarnes2]

I think the magic word you are looking for is "read groups".

It's a tag that you can add to your .sam file, so that one .bam file can have projects mixed in, but distinguishable. You'll have to poke around at different software to find out how to add them to your .bam file after making it. In the future, you can make sure that they are written into your .bam file as you are making it.