Question: How to quantify PCR duplication from bam file
0
gravatar for simplitia
2.9 years ago by
simplitia40
simplitia40 wrote:

Hi I know that I can mark and remove duplicate using picard. However is there way I can quantify how much duplication I have? So for example lets say I have file1.bam - mark and remove duplication resulting in file2.bam

now what I like to do is quantify pcr duplication for file1.bam and file2.bam this way I can then compare the two before and after and make sure what I did it correct.

thanks!

rna-seq • 1.4k views
ADD COMMENTlink modified 2.9 years ago by genomax92k • written 2.9 years ago by simplitia40
1

After searching around a bit the solution is to use samtools flagstat; this works for me in case someone else stumbles on to this thread. thanks.

ADD REPLYlink written 2.9 years ago by simplitia40
0
gravatar for genomax
2.9 years ago by
genomax92k
United States
genomax92k wrote:

Take a look at this thread for answers to your questions. You do not need to align the data to use clumpify.sh which is a big advantage.

ADD COMMENTlink written 2.9 years ago by genomax92k
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