Question: (Closed) Multiple Reads Mapped To The Same Position
gravatar for KCC
7.8 years ago by
Cambridge, MA
KCC4.0k wrote:

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?

sam • 1.7k views
ADD COMMENTlink modified 7.8 years ago by Sukhdeep Singh10k • written 7.8 years ago by KCC4.0k

Closed as a duplicate.

ADD REPLYlink written 7.8 years ago by Zev.Kronenberg11k

I see what you mean - just make sure to link to the original

ADD REPLYlink written 7.8 years ago by Istvan Albert ♦♦ 84k

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?

ADD REPLYlink written 7.8 years ago by KCC4.0k
gravatar for Sukhdeep Singh
7.8 years ago by
Sukhdeep Singh10k wrote:

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.


ADD COMMENTlink written 7.8 years ago by Sukhdeep Singh10k
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