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LangilleLab / microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
GNU General Public License v3.0
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missing double dash in command line vsearch #2

Closed dridk closed 7 years ago

dridk commented 7 years ago

You forgot double dash everywhere. For instance : 

  vsearch -derep_fulllength stool_sequences.fasta -output cluster/unique.fasta -sizeout -minseqlength 50
  vsearch --derep_fulllength stool_sequences.fasta --output cluster/unique.fasta --sizeout --minseqlength 50
gavinmdouglas commented 7 years ago

I'm not sure I follow - are you referring to our wrapper script "chimera_filter.pl"? If you're referring to vsearch itself the GitHub page is here: https://github.com/torognes/vsearch

dridk commented 7 years ago

Oups.. I was too fast ! Sorry ! I fogot to mention where does it take place ! On the wiki => https://github.com/mlangill/microbiome_helper/wiki/16S-tutorial-for-CCBC

dridk commented 7 years ago

From the vsearch documentation, it's : 

  vsearch --derep_fulllength

And not : 

  vsearch -derep_fulllength
gavinmdouglas commented 7 years ago

Thanks for pointing that out, I switched to "--" for clarity.