summary.seqs

Commands in mothur
1

Hi all.

I am completly neat using mothur. I have just got my sequences back yesterday and I exicited about that! I gotsff, fna and qual files.

  • The first thing I would like t do is to have a look to how the look using FastQC, but I need fastq format for this approch and I can’t convert it using windows. Any suggestions?
    -I am trying to run summary.seqs command but I can’t with fna file, just If I extract the FASTA from sff using sffinfo…is that normal? Could you run summary seqs for all the samples at the same time?
    -The first step would be the denoising. I gues we need a high performance computing cluster…as this step tends to take the longest, is that right?

We are working with datas from 350 samples, and we got 900.000 reads in the first run.

Thanks for your help

2

I’d encourage you to check out our 454 SOP (http://www.mothur.org/wiki/454_SOP) and go from there. If you have more specific questions, I’d be happy to answer them. We also have a make.fastq file that takes in fasta and quality score files.

Pat