sequences removed during shhh.flows

Commands in mothur
#1

What are the criteria for sequences to be removed during shhh.flows? I’ve been walking back through the SOP trying to figure out which steps are resulting in significant reduction of reads. Below are the numbers of reads that I have a several of the initial steps

sffinfo(sff=GM0HNNG06.sff, flow=T) -Count # of flows in GM0HNNG06.flows with grep 141281

trim.flows(flow=GM0HNNG06.flow, oligos=GM0HNNG06.oligos, pdiffs=2, bdiffs=1, minflows=320, maxflows=450, processors=4) -# flows in GM0HNNG06.trim.flows 97168

shhh.flows(file=GM0HNNG06.flow.files, processors=4) - # seqs in GM0HNNG06.shhh.fasta 59741

What is the criteria that shhh.flows uses to discard sequences? Is there a scrap file that gives the error codes for this step?

p.s. I’m using a lower minflows because my pcr products are 350-450bp

#2

No sequences are removed during shhh.flows. If you see a reduction, that’s likely becuase they’re now in the names files.

Pat

#3

that’s it, thanks. I didn’t think to look in the names since the command doesn’t ask for a names file