Question: Counting number of duplicated reads from fastq file
5.1 years ago by
Brian Bushnell ♦ 17k
Walnut Creek, USA
Brian Bushnell ♦ 17k wrote:
If you want to deduplicate raw paired fastq files, I recommend trying
dedupe.sh from the BBMap package. You can run it like this:
dedupe.sh in1=read1.fq in2=read2.fq out1=x1.fq out2=x2.fq ac=f
That will also print the exact number of duplicates removed.
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