I am trying to clean my MiSeq sequences more thoroughly than in the MiSeq SOP by using the following command after making contigs:
screen.seqs(fasta=filename.trim.contigs.fasta, contigsreport=filename.contigs.report, mismatches=5, minoverlap=25, group=filename.contigs.groups, processors=1)
I have several samples, and in every case I am getting the following error (example numbers):
“[ERROR]: found 101388 sequences in your fasta file, and 101386 sequences in your contigs report file, quitting.”
How can I get the command to work?