Hi All,
I have 16s rRNA sequences and I am analyzing it using mothur, I used the following commands:
align
filter
dist
cluster
I am wondering ids it necessary to use chimera commands to remove chimears.
Please help, I have done it without removing chimeras and if we have to remove what should I do.
Yes. It is critical that you remove chimeras. Please follow the SOP and see where they fit into the overall picture.
Thanks,
So, I looked at SOP and there the chimeras are removed after preclustering, I didn’t do preclustering. I tried using it with my original unique fasta sequences(7728 sequences) using following command:
chimera.uchime(fasta=/g1/home/sulbha/MothurSoil/sample_all.unique.fna, name=/g1/home/sulbha/MothurSoil/sample_all.names)
and the result says
It took 171 secs to check 7728 sequences. 0 chimeras were found.
It this correct or I am missing something.
It’s really hard to diagnose what might be going on here without additional information. What else are you doing in the pipeline to this point? Why not use pre.cluster? What type of data are these? Why aren’t you following hte SOP?