I'm conducting fungi community analysis for the first time. I'm basically following this tutorial.
So far, I've only used the forward sequence of ITS1 primer (515F 5'-GTGCCAGCMGCCGCGGTAA)
I used DADA2 to denoise with these parameters:
and the UNITE dB (unite-ver7-99-seqs-01.12.2017) for taxonomic identification
Of the total ~8,600 entries, only ~2,000 (less than 25%) were identified to a taxonomic level of order and below, whereas the remaining were only identified up to class or Phyllum (fungi) levels,
Is this expected? Is there any advice to improve the classification? for instance, during the denoise process
Fungi are less well studied than bacteria and ITS reads can vary in length, and this combination of reduced database coverage and variable length makes ITS classification perform worse than 16S classification at times. The short length of your reads specifically (150 bp total) would also reduce taxonomic resolution.
Try using the new UNITE V8, which should be better than V7!