I was having trouble with the trim.flows command having merged my 41 sff files and have just realised that the stupid sequence provider has removed the barcodes from my samples, hence the reason everything is being scrapped. Can someone please tell me whether it’s possible using mothur to proceed with the 454 SOP given that my sequences have all been stripped of barcodes? Surely there’s a way of telling it which sequence is from which sample.
Thanks in advance
If each file represents a single sample, then the easiest way to go about this would be to denoise/quality filter each file, then create a groups file for each sample (make.group).
Once you have a set of fasta/group pairs, the workflow to unify everything will be:
- Concatenate the fasta files together
- Concatenate the groups files together
- Rununique.seqson the new fasta file. This will create a names file and a *.unique.fasta file.
- Runcount.seqson the names file and the groups file. This will create a *.count_table file.
From there, you can take your *.unique.fasta and *.count_table through the rest of the SOP (alignment, chimera checking etc).