Full UNITE+INSD dataset for Fungi

[shashankgpt]

Hi,
I was wondering about which database should we use for ITS sequence analysis, UNITE or UNITE+INSD dataset?
Is the UNITE+INSD dataset stable?

Secondly, I got an error while training the UNITE database

qiime tools import --type 'FeatureData[Sequence]' --input-path sh_refs_qiime_ver8_dynamic_s_02.02.2019_dev.fasta  --output-path unite.qza
Imported sh_refs_qiime_ver8_dynamic_s_02.02.2019_dev.fasta as DNASequencesDirectoryFormat to unite.qza

qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path sh_taxonomy_qiime_ver8_dynamic_s_02.02.2019_dev.txt --output-path unite-taxonomy.qza
Imported sh_taxonomy_qiime_ver8_dynamic_s_02.02.2019_dev.txt as HeaderlessTSVTaxonomyFormat to unite-taxonomy.qza

qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads unite.qza --i-reference-taxonomy unite-taxonomy.qza --o-classifier classifier.qza
Plugin error from feature-classifier:

  Invalid characters in sequence: ['a', 'c'].
  Valid characters: ['Y', 'N', 'S', 'R', 'A', 'T', 'H', 'G', '-', 'M', 'D', '.', 'W', 'V', 'K', 'C', 'B']
  Note: Use `lowercase` if your sequence contains lowercase characters not in the sequence's alphabet.

Debug info has been saved to /tempFolder/qiime2-q2cli-err-n5gln933.log

[Nicholas_Bokulich]

Hi @shashankgpt,

@shashankgpt

I was wondering about which database should we use for ITS sequence analysis, UNITE or UNITE+INSD dataset?

That is really a matter of personal taste/scientific decision-making.

@shashankgpt

Is the UNITE+INSD dataset stable?

As far as I know the UNITE releases with UNITE+INSD are stable, but you should probably check the UNITE website for more specifics.

@shashankgpt

Invalid characters in sequence: ['a', 'c']. Valid characters: ['Y', 'N', 'S', 'R', 'A', 'T', 'H', 'G', '-', 'M', 'D', '.', 'W', 'V', 'K', 'C', 'B']

Yep, this error is quite common and is known to occur with some releases of UNITE. This tutorial has an example of using UNITE, including a bash one-liner to remove lower-case characters:

Fungal ITS analysis tutorial

Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a QIIME 2 workshop in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the q2-itsxpress tutorial for other fungal ITS analysis options in QII…

Good luck!