I found a problem with my analysis of skin microbiota. My reads are sequenced by Illumina MiSeq (2x300). I performed the following steps:
- qiime feature-classifier classify-sklearn using SILVA 132 database
I obtained the attached taxonomy.qza file. After manual inspection, a lot of reads were classified as ‘Bacteria’ with no further assignation below this taxa rank. I performed BLAST over some of those reads, and matched with Homo sapiens DNA. I believed that after SILVA classification, all assigned to Bacteria were indeed bacteria. Maybe I missed a filtering step of human reads? I followed the tutorials of the qiime2 website, but I didnt see that.
Thanks a lot
taxonomy-silva.qza (170.4 KB)