trim.seqs-problem with qfile

Commands in mothur
1

Hello,
I have data from 454 pyrosequencing. I used for denoising my data: mothur > shhh.flows(flow=sample.flow, order=B, LookUp_Titanium.pat). Outputs were used in next step with the command “trim.seqs” and parameter “qaverage”: mothur > trim.seqs(fasta=sample.shhh.fasta, qfile=sample.shhh.qual, qaverage=25). Program wrote “Error in reading your qfile, at position -1. Blank name” and mothur falled down. Could somebody help me with this problem? Many thanks.

2

If you’re doing shhh.flows, you don’t need to run trim.seqs with quality score values. The shhh.flows qscore values are pretty meaningless. Checkout the pipeline at https://mothur.org/wiki/454_SOP

Pat

3

Many thanks.
Helen