FastUniq "error in open left fastq file for read!"

Question

[ae75]

I'm getting the following error with FastUniq (running for PE sequences, testing with just one pair):

Error in open left fastq file *FULL TEXT OF FIRST READ IN FIRST FILE* for read!

There are a few other complaints of this problem scattered on the web but none have even a suggestion for solving it. Does anyone have any ideas for how to resolve this issue? Or, alternatively, want to suggest another tool for filtering duplicates in fastq format?

Answer 1

[Brian Bushnell]

You can use Dedupe from the BBMap package instead. Usage:

dedupe.sh in1=r1.fq in2=r2.fq out=nodupes.fq

For paired input, the output will be interleaved, but you can deinterleave it with reformat.sh if you want.