How to quantify PCR duplication from bam file
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!
• 2,926 views
•
link
updated
by
GenoMax
•
written
by
simplitia •
•
written
by
simplitia •
1 answer
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.
Log in to answer this question.
More posts like this
-
remove duplicates in Nanopore cDNA PCR data
written by 静 •
-
Size of Output BAM file bigger than the SUM Size of Input files after merging with samtools
written by Giggle •
-
Transcriptomic assembly Stringtie
written by Nelislam4 •
-
Mark duplicate "Picard"
written by Nelislam4 •
-
shall we consider -- keep-dup all when we removed duplication?
written by star
-
Did my CHIP-seq analysis right?
written by mikysyc2016
-
I would like to compare my RNA seq file together to find overlap?
written by star
-
Picard vs samtools rmdup
written by xd_d
-
Picard Mark Duplicate Reads In Galaxy
written by Tonyzeng •
-
Samtools Rmdup And Picard Mark Duplicates
written by Kssr
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.