Dedupe paired end example

[Seigfried]

Hi Brian

Could you please guide me to removing duplicates using paired end data?

I want to modify dedupe.sh in=X.fa out=Y.fa outd=duplicates.fa

I am aware that this does not currently support Containment

However, I would get a lot more trouble later on if my paired reads don't match up after individual dedupeing.

[Brian Bushnell]

Hello Niranjan,

You can use Dedupe like this:

dedupe.sh in1=read1.fq in2=read2.fq out=deduped.fq outd=duplicates ac=f

The pairs will be kept together. The output file will be interleaved. You can de-interleave it like this:

reformat.sh in=deduped.fq out1=deduped1.fq out2=deduped2.fq

-Beian