Hi Laura, QIIME 1.8.0 isn't supported anymore - you should really be using QIIME 1.9.1. My suggestion here should work for both versions, but if not you should first upgrade your version (or switch to QIIME 2, as QIIME 1.9.1 won't be support anymore as of January 1, 2018.
We don't have a direct way to filter sequences based on their length for Illumina data, but during quality filtering with split_libraries_fastq.py this can be achieved by setting the --min_per_read_length_fraction parameter. This sets how long a read must be, as a fraction of it's starting length, to be retained after quality trimming.
A more direct way to achieve your goal though is probably just to filter OTUs that are unassigned using filter_taxa_from_otu_table.py
. This would let you still retain OTUs with shorter representative sequences that achieved a good taxonomic assignment, and also remove OTUs with longer representative sequences that don't achieve a good taxonomy assignment. You'll need to define what it means for a result to be assigned - for example passing -p k__Bacteria,k__Archaea
would allow you to retain only OTUs that were at least assigned to the kingdom level (if you've assigned against the Greengenes taxonomy).
Hope this helps!