working with single end reads

Commands in mothur
6

This is a repost of an older thread. I was doing something similar when I started with Ion Torrent data analysis SOP that do not exist anymore (ho boy that does take me back…)

But from this thread: Processing MiSeq single (unpaired) reads

" A basic workflow is

  1. Runfastq.info over each fastq file to split them into fasta and qual files.
  2. Quality filter them withtrim.seqs .
  3. Merge the QC-ed fasta files together withmerge.files to get your full fasta file.
  4. Create a groups file usingmake.group .
  5. Rununique.seqs to dereplicate the fasta file.
  6. Runcount.seqs over the resulting names file, and your groups file, to get the count table.

From there, you should be able to go back to the MiSeq SOP at the alignment step using the *.unique.fasta file and the count table."

1 Like