I have finally decided to jump on the hype train and use QIIME 2 to analyze some data. So far, I am a fan of QIIME2 and all it can do, and I have been following the Overview tutorial to analyze some data, but I have encountered a few issues, as I can’t seem to find the right place to answer my questions.
To give you a little background, I am analyzing 18S amplicon sequences, and I have generated my .fastq file with Ion Torrent PGM, I performed demultiplexing in QIIME(1) with split_library.py, imported my .fna seqeunces file into QIIME 2 and finally dereplicated my sequences and used classify-sklearn against the 132 SILVA release to assign taxonomy to my sequences. Here are my concerns:
- Is it possible to receive an ASV separated table (with assigned taxonomy similar QIIME(1) format) from my generated FeatureData[Taxonomy] artifact? In other words, how can I convert my artifact to show the original ASVs that were collapsed to form the taxonomy I see in FeatureData[Taxonomy] after performing a taxonomic visualization (e.g. with bar plots)?
- Is it possible to ‘normalize’ my table for ununiform sequencing depth (if or if not converted to the format above)? I believe it’s possible to export the artifact into an editable form and change it manually, but is there a way to do that in QIIME2?
- I originally used sampleIDs with underscores, can I edit that to a different character in QIIME2 within the generated FeatureData[Taxonomy] artifact?
Thank you for your time and patience. Please let me know if I can provide any more detail or clarify any of my questions