missing a step in MiSeq SOP

Commands in mothur
1

Hi, while I follow all steps in MiSeq SOP, I guess a step is missing for generating file:
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.count_table

This file is used in step ‘classify.seqs’, but the previous steps only created:
list.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta
list.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.chimeras
list.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.accnos

Can someone tell me how to generate file stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.count_table?
Thanks a lot.

2

That should be created in the chimera.uchime command if you run it as stated on the wiki.

Pat

3

Ihave the same problem and itdoenst creat that file :S

4

Hey,
You might want to try adding the count file to the chimera check.
chimera.uchime(fasta=yourfile.fasta, count=yourfile.count_table, dereplicate=t)

Hope it helps,

Carla