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torognes / vsearch

Versatile open-source tool for microbiome analysis
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Remove chimeras from count_table #322

Closed rtrpaine closed 6 years ago

rtrpaine commented 6 years ago

Hello,

I am using mothur (v1.39.5) 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

As a possible solution, I created a fasta file with the chimeras in it. Could I simply turn this into an .accnos file and use the accnos file to remove the chimeras from the count_table?

rtrpaine commented 6 years ago

I have solved the problem, so I am closing the issue.