Is there a way to identify replicates and retain their indices in fastq records?
I have used Shortread and BiostrinG to read a fastq file, and used tables() to identify duplicates. However, it's not possible to recover the indices of the reads, which I would need for further analysis. This is what I have tried:
tb = tables( readFastq(fastqfile) )
Trying to run a *apply loop would take forever to finish.
Thanks for any pointers
1 answer
You can use clumpify.sh from BBMap suite to mark sequence duplicates. See in-line help and this post for more information: A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files
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