How to merge replicates of mapped reads out of Tophat for pathview and gage analysis.
2
0
Entering edit mode
6.8 years ago
Parham ★ 1.5k

Hi, I have three biological replicates for my experiment. I wonder how should I merge the accepted_hits.bam out of Tophat for doing Pathview/gage analysis for this workflow? Let's name the accepted_hits.bam replicates as 1.bam 2.bam and 3.bam for the sake of short writing. 

Tophat gage pathview replicates • 2.3k views
ADD COMMENT
0
Entering edit mode
6.2 years ago
s.vdrzeeuw • 0

use bam_merge from tophat itself or use sambamba merge or samtools merge.

ADD COMMENT
0
Entering edit mode
6.2 years ago

You can merge any bam files using samtools merge or using picard BUT Why do you want to merge biological replicates ?

ADD COMMENT

Login before adding your answer.

Traffic: 1637 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6