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: kalydeco.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.taxonomy
Total number of sequences = 2,287,993
While for file:
kalydeco.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.tax.summary
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(list=xxxx.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.list, count=xxxx.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.pick.count_table, taxonomy=xxxx.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.pick.taxonomy, 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,
K