Subsampling metagenomics reads via reformat.sh

Question

[serene.s]

Hi Guys! I am using reformat.sh for subsampling my metagenome samples but I wanna know what does the parameter "sampleseed" do to the reads? Is it alright if I just use the samplereadstarget without using the seed value?

command used: reformat.sh in=file_R1.fastq.gz in2=file_R2.fastq.gz out=file_subsampled_R1.fastq.gz out2=file_subsampled_R2.fastq.gz samplereadstarget=10889622

Thanks in Advance Saraswati

Answer 1

[GenoMax]

sampleseed is used as a seed if you want to get deterministic i.e. identical datasets for multiple runs of reformat.sh. Otherwise you may get a different set of reads everytime. If you are not interested in getting an identical dataset (which is why you may be sampling) then do not set an identical seed value for multiple runs.

[serene.s]

thanks GenoMax