Remove sequence groups

Commands in mothur
1

Hi,
I have a sff file (allData.sff) with 10 samples (with different barcodes). I’m only interested in analyzing 4 of those 10 groups…
Can you tell me how to remove those groups, and when (during the pipeline)? Can I create a sff file with only those 4 groups?

Thank you!

Cheers,
Joana

2

When you’re running the trim.flows command you could just use an oligos file that only includes the barcodes of the groups you’re interested in.

Or if you’d rather QC all your sequences first, you can use the get.groups (or remove.groups functions on your fasta file and count/shared file.

3

Thanks! I’ll try that.