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Old 10-31-2016, 08:52 AM   #1
mcrawford
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Default FastQ: trimming paired reads down to a set length

Hello,

I have some 2x300bp sequencing data and I want to treat it as if it were a 2x100bp run.

So, I have some paired-read FastQs with reads of all different lengths, up to 300bp. I want to trim them so that they are all less than or equal to 100bp in length.

Is this possible and what would be the easiest way to do it?

Alternatively if the longer reads could be cut up so they are split into different reads of roughly 100bp (e.g. 200bp read gets cut into two 100bp reads), that would be even better, but I'm not sure of this is possible.

Very many thanks for any help.
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Old 10-31-2016, 08:57 AM   #2
GenoMax
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Easiest would be to use bbduk.sh from BBMap suite with option forcetrimright=99
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Old 10-31-2016, 10:11 AM   #3
mcrawford
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Quote:
Originally Posted by GenoMax View Post
Easiest would be to use bbduk.sh from BBMap suite with option forcetrimright=99
Thanks very much for the reply, this works

In case this helps anyone else, I am on Windows, so I run BBDuk like this:
java -ea -Xmx200m -cp C:\bbmap\current\ jgi.BBDuk2 in1=Sample_R1.fastq in2=Sample_R2.fastq out1=SampleTrimmed_R1.fastq out2=SampleTrimmed_R2.fastq ftr=99
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