How to merge replicates of mapped reads out of Tophat for pathview and gage analysis.

Question

[Parham]

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.

Answer 1

[s.vdrzeeuw]

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

Answer 2

[GouthamAtla]

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