yak count question with paired reads

[scottgeib]

Under "getting started" on readme page, it describes:

for paired end: to provide two identical streams

./yak count -b37 -t32 -o sr.yak <(zcat sr.fq.gz) <(zcat sr.fq.gz)

What is the reason to feed the same reads to yak twice as identical streams? Or is this meant to be R1 and R2 read pairs as separate streams?

[lh3]

yak count needs to read the input twice but a stream can be only read once.

[scottgeib]

Thanks Heng! So the input should be both the F and R paired read files streamed twice together?

So in a folder containing test.R1.fastq.gz and test.R2.fastq.gz it would be :

yak count ….. < (zcat fastq.gz) < (zcat fastq.gz) #same set of files streamed twice (so yak can find read pairs, one from each stream) not yak count ….. < (zcat R1.fastq.gz) < (zcat R2.fastq.gz). # one stream of forward and one stream of reverse (in this case yak would be assuming paired read files, which yak does not assume)

From: Heng Li @.> Reply-To: lh3/yak @.> Date: Monday, August 30, 2021 at 12:29 PM To: lh3/yak @.> Cc: "Geib, Scott" @.>, Author @.***> Subject: Re: [lh3/yak] yak count question with paired reads (#10)

yak count needs to read the input twice but a stream can be only read once.

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[lh3]

So the input should be both the F and R paired read files streamed twice together?

Yes