Question

Mark duplicate "Picard"

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4.5 years ago

Nelislam4 ▴ 20

Hi, I am wondering, How mark duplicate of Picard tools works? In other words. How Picard tools detect the duplicated read in BAM file?

coz I actually have replicates of the same RNA-seq samples, and I just want to run differential expression analysis for those samples but I don't know If merging those BAM files and mark the duplicate by Picard tools would solve the issue or not?

Please Help.

RNA-Seq • 1.3k views

ADD COMMENT • link updated 4.5 years ago by ATpoint 81k • written 4.5 years ago by Nelislam4 ▴ 20

score 3 · Answer 1 · 2019-10-04

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4.5 years ago

ATpoint 81k

You should not mark duplicates in RNA-seq, please use the search function on why that is. If you have technical replicates (=same RNA/cDNA sequenced multiple times) you can either merge the BAM files prior to quantification or sum up the columns of the count matrix. DESeq2 afaik has a function to do that as well.

ADD COMMENT • link 4.5 years ago by ATpoint 81k

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In addition to that, it's not because you have technical replicates that you will end up with read duplicates.