split.groups to get fasta files including duplicate sampels

Hello together,

I have a question regarding the split.groups command.
At a certain step of the processing (just after removal of all unwanted seqs and before final clustering in the MiSeq SOP) I’d like to extract the fasta files for each sample separately. When doing it like this:

split.groups(fasta=XXX.fasta, count=XXX.count_table),
where the count_table contains group information and the number of duplicate sequences for each unique sequences.

it only splits out the unique sequences for each group/sample. However, I would like to get all sequences per group/sample in a file.
I do not really know where the mistake is/how to solve that issue.

Any help would be greatly appreciated.
Thank you very much!


You can use the deunique.seqs command to generate a fasta file that contains the duplicate sequences. https://mothur.org/wiki/Deunique.seqs

Hi Sarah,
thank you very much. Sorry for my ignorance. Did not really see that command…