Question: How to merge replicates of mapped reads out of Tophat for pathview and gage analysis.
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gravatar for Parham
4.7 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

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. 

gage pathview tophat replicates • 1.8k views
ADD COMMENTlink modified 4.1 years ago by geek_y9.3k • written 4.7 years ago by Parham1.4k
0
gravatar for s.vdrzeeuw
4.1 years ago by
s.vdrzeeuw0
Netherlands
s.vdrzeeuw0 wrote:

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

ADD COMMENTlink written 4.1 years ago by s.vdrzeeuw0
0
gravatar for geek_y
4.1 years ago by
geek_y9.3k
Barcelona/CRG/London/Imperial
geek_y9.3k wrote:

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

ADD COMMENTlink written 4.1 years ago by geek_y9.3k
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