Sub sampling from pyrosequencing reads

Question

[Sandy]

I have a pyrosequencing reads from almost 200 samples, obviously in one .fna file. I want to do subsampling from there in a way to have equal no. of sequence (randomly) from each sample. Does any one know any script/ programme to do that.

Answer 1

[Prakki Rama]

This Biostar post should be useful to you.

[Sandy]

Thanks Prakki Rama, But I was also wondering that, does this give me the equal no of sequences from each sample ?

[Prakki Rama]

Yes. It generated random number of sequences equally in all my files. I ran the following to get multiple files in shell.

for((n=1; n<=10; n=n+1)); do sh subsample_se_fasta.sh sample.Seq.fa s_sub_"$n".fasta 10; done

[Sandy]

Thanks for your quick response.

[Sandy]

Actually I have .fna file and I want to subsample it before picking OTU from there.