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Old 02-24-2015, 11:35 AM   #9
jpummil
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Location: Fayetteville, AR

Join Date: Apr 2014
Posts: 82
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Hey Brian!

So, to subsample a set of PE reads to reduce overall file size (creating quick running data set for a workshop), this would suffice?

reformat.sh in1=x1.fq in2=x2.fq out1=y1.fq out2=y2.fq reads=-1 samplerate=0.1 int=f

It would: Keep parings intact, give me 1/10 the data overall, ensure no interleaving (though I expect assigning the pairings at the beginning would do this as well)

I already did a quick quality trimming with:
reformat.sh in1=x1.fastq in2=x2.fastq out1=y1.fastq out2=y2.fastq outsingle=singletons.fq qtrim
=rl trimq=10 minlength=50

Edit: Seems to have worked!

-rw-rw-r-- 1 jpummil jpummil 2.0G Feb 24 13:06 L001_R1_001_Qt.fastq
-rw-rw-r-- 1 jpummil jpummil 2.0G Feb 24 13:06 L001_R2_001_Qt.fastq

-rw-rw-r-- 1 jpummil jpummil 199M Feb 24 13:43 L001_R1_001_Sub.fastq
-rw-rw-r-- 1 jpummil jpummil 199M Feb 24 13:43 L001_R2_001_Sub.fastq

And it ran just fine in SPAdes.

Last edited by jpummil; 02-24-2015 at 11:59 AM. Reason: New info...
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