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

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?

assembly rna-seq
• 3,625 views • link
updated by Ram Ram • written by ae75 • ae75

1 answer

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.

• 0 views • link
updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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