HI all,

This has been my first run through using miseq data and mothur.

I have gone through to the end of the miseq SOP using my own data. I am sure due to my inexperience my outputs appear unusual:

For file:
Total number of sequences = 2,287,993

While for file:
Total number of sequences = 101,988

I thought these should be the same.

I know I have done something wrong somewhere. I have to edit down by one “pick” input files name for some commmands to work.

eg : classify.otu(, count=xxxx.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.pick.count_table,, label=0.03)

I had to modify the input file name by deleting the underlined “pick” as I did not have files with these exact names.

Well lets hope this makes some sense!

Thank you in advance for your help,


What files and where in them are you getting these numbers from?