Sub-sampling paired-end reads

[Moritz E. Beber]

I realize that you haven't worked on this tool in a long time and probably moved on to other things.

However, I was curious what you think about sub-sampling paired-end reads? These usually data come in separate files x_1.fastq and x_2.fastq so if I applied your program separately different reads would be selected breaking the pairs, as far as I understand.

Thanks for any ideas.

[Moritz E. Beber]

Apparently, the way that seqtk handles this, for example, is by using the same seed for each pair file. I guess the same would work here?

[Haruka Ozaki]

Sorry for my late reply. Thank you for asking.

by using the same seed for each pair file

That's right!

[Moritz E. Beber]

Thanks for confirming. 🙂