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