I would like to know how many contigs I have in each one of my samples when I have processed all the steps. In example: sample A has 152200 sequences, sample B 155500.
I think it easy but I did not find how to do
The initial number of contigs per sample it is written in the log file.
If you mean after all cleaning, pre-clustering, clustering, etc, that would be just if you add all counts per sample… if you have your count table, it is just adding all numbers from each OTU/ASV/Whatever from each sample. You can do it in excel or awk
I know I can use the excel since the OTUs distribution but I mean with a mothur tool
Thanks Leocadio
Try count.groups on your final shared file
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