search

mothur / mothur

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
www.mothur.org
GNU General Public License v3.0
261 stars 110 forks source link

Vsearch question #484

Closed rtrpaine closed 6 years ago

rtrpaine commented 6 years ago

Hello,

I don't know if this is an appropriate place to ask advice on this issue, so forgive me if it's not. I am using mothur to analyze MiSeq data related to fish metabarcoding (12S rRNA). I am working off of my schools supercomputer via remote access with a PuTTY. I am currently trying to remove chimeras from my dataset.

Due to the nature of running mothur on Linux, my schools computer guy can not put the vsearch executable on the server, which is required to run the chimera.vesearch command. He did, however, upload the vsearch algorithm to the server and I have been able to use it to directly remove chimeras from my .fasta file. This issue I am having is trying to remove the chimeras from my associated count_table. Can this be done in vsearch? If so, can someone explain or point me in the right direction?

Thanks,

Robert

rtrpaine commented 6 years ago

Hi,

I have found the Vsearch GitHub page So, I will close this issue and re-post it there.

Cheers!