Question: Mark duplicate "Picard"
gravatar for Nelislam4
10 months ago by
Nelislam40 wrote:

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 • 413 views
ADD COMMENTlink modified 10 months ago by ATpoint36k • written 10 months ago by Nelislam40
gravatar for ATpoint
10 months ago by
ATpoint36k wrote:

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 COMMENTlink written 10 months ago by ATpoint36k

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

ADD REPLYlink written 10 months ago by WouterDeCoster44k

Thanks for your help

ADD REPLYlink modified 10 months ago • written 10 months ago by Nelislam40
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