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

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.

replicates pathview gage tophat

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updated 4.8 years ago by Ram

• written 12.1 years ago by Parham

2 answers

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

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updated 4.8 years ago by Ram

• written 11.5 years ago by s.vdrzeeuw •

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

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updated 4.8 years ago by Ram

• written 11.5 years ago by GouthamAtla

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