Question: How To Color The Reads In Bam Files
0
gravatar for troym2026
4.8 years ago by
troym20260
troym20260 wrote:

I wanted to merge two BAM (alignements) files together. Before merging, how can I color the reads in the BAM files so that while viewing at the UCSC Genome Browser I can tell the reads apart from the two files? Thanks!

alignment bowtie bam • 1.2k views
ADD COMMENTlink modified 4.8 years ago by Ashutosh Pandey11k • written 4.8 years ago by troym20260
1

IGV might work better than the UCSC genome browser for your application.

ADD REPLYlink written 4.8 years ago by donfreed1.3k
0
gravatar for Ashutosh Pandey
4.8 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

Don't merge the BAM files if you want to visualize them using different colors in UCSC genome browser. The UCSC color settings can not be controlled from/within the BAM file. You should upload them separately and change color settings in their config files that goes along with the bam files in UCSC genome browser. I have never done something like this before so I am not sure if it can be done but this page should be able to help you : https://genome.ucsc.edu/goldenPath/help/bam.html

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Ashutosh Pandey11k
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