How to get no. of unique sequences coming from each sample?

Commands in mothur
1

Hi,

How can I get no. of unique sequences coming from for each sample? Second question, Is there a way to remove the sequences occurring only once in whole data set even before unique.seqs step?

Thanks for help,
Richa

2

How can I get no. of unique sequences coming from for each sample?

mothur > split.groups(fasta=yourFastaFile, count=yourCountFile) - creates individual files per sample
mothur > summary.seqs(fasta=yourFastaFileForEachSample) - unique sequences in each sample
mothur > summary.seqs(fasta=yourFastaFileForEachSample, count=yourCountFileForEachSample) - unique and redundant sequences for each sample

Is there a way to remove the sequences occurring only once in whole data set even before unique.seqs step? You can use the split.abund command to separate sequences by abundance. For example:

mothur > split.abund(fasta=current, name=current, cutoff=1)