fastq, fasta and qual

Commands in mothur
1

Dear mothur team,

This is the first time I work with mothur and I am finding some problems to start. I was wondering if anyone could shed some light on how to proceed.

I have two Illumina runs that I need to work with. Forward and reverse sequences have already been merged by the company, so that I only have one .fasta and one .qual file per run (no R01 and R02 available), and all samples are within them. How can I start analysing my data?

I will appreciate any insight you may have.

Thanks!

Lin.

2

The company should have guides to tell you how to split out each sample

3

Thank you so much for your prompt answer!
I have contacted the company and I am waiting for an answer. In the case I end up with single .fastq files for each sample, where fwd and rev reads have been merged, how could I proceed with the analysis?

If not, could I use the 454 SOP (at least trim.seqs), since I have a .fasta and a .qual file, and I could provide the .oligos?

Thank you so much for your help!

L.