shhh.seqs - duplicated seqs

cjrobinson3 · August 23, 2011, 1:51pm

Hi all,

When I run shhh.seqs --> shhh.seqs(file=GM2BZH101.flow.files, processors=8), the resulting GM2BZH101.shhh.fasta file contains 628 sequences that are duplicated. The sequences are not duplicated in the .fna files generated by the FLX software. Also, I’ve run shhh.seqs on four flow.files and this only happened with two of them, which are from the same run.

Does this indicate a problem with my sff and/or flow.files from this run?

Thanks guys!

cjr

pschloss · August 25, 2011, 8:17pm

shhhhhhh, no one knows about this command yet

You should also have a GM2BZH101.shhh.names file that indicates the names of the sequences that are redundant to the denoised sequences.

Pat

Topic		Replies	Views
shhh.flows and editing results Commands in mothur	1	2331	November 8, 2011
Different seqs in fasta and qual afer shhh mothur bugs	7	6444	December 20, 2012
trim.flows and shhh.flows on Junior+ data Commands in mothur	1	1619	January 21, 2015
shhh.seqs Commands in mothur	2	2387	May 30, 2012
shhh.flows output is very small! What's wrong? Commands in mothur	5	3299	April 3, 2014

shhh.seqs - duplicated seqs

Related topics