Using my own code, I would like to detect if tags are duplicated.
I wrote a script that tallies the number of tags which map to every position, with a different tally for the forward and reverse strands. For all positions that have multiple tags mapped to it, I keep one and discard the rest.
The count I get of duplicated reads is not the same as samtools rmdup.
Is there something extra that I am missing that samtools rmdup does?
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written
by
KCC
1 answer
Is it more or less, if the number is more from rmdup, then I have a feeling its not working strand specifically.
Also, from the FAQ page of Picard Toolkit, where you also have a tool for duplicates called MarkDuplicates (whose output you might wanna compare)
Q: What is the difference between MarkDuplicates and samtools rmdup? A: samtools rmdup does not remove interchromosomal duplicates. MarkDuplicates does remove these duplicates.
So, might be one of the reason.
Cheers
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Closed as a duplicate.
I see what you mean - just make sure to link to the original
How is this a duplicate question? I am asking how to write code that finds duplicate reads. I am not asking how to use existing code to remove duplicates?