Large portion of Cyanobacteria

[SoilRotifer (Mike Robeson)]

@Sabrin

Does --p-min-lens 900 1200 1400 means i am loosing any ref. sequences less than 1200 bp for 16S, could that be limiting my classifier to full length ref. 16S?

This is explained in the RESCRIPt documentation here, as well as the help text, which you can access by:

qiime rescript filter-seqs-length-by-taxon --help

@Sabrin

Would lowering that increase my chances and my ref. seq. by including shorter amplicon reads?

Potentially. You can play around with the settings. If you do not need to differentially length-filter the sequences by taxonomy, you can simply use qiime rescript filter-seqs-length ... instead. This way you can trim everything down to 900 bases, or whatever length you choose.