how to convert FeatureData[RNASequence] to FeatureData[Sequence]

[the_dummy]

Hello,

I would like to use filter-seqs-length-by-taxon to discard archea and bacteria to generate a database consists of only eukaryota. To achieve this, I have downloaded silva 138 with the command below.

qiime rescript get-silva-data --p-version 138 --p-target SSURef_NR99 --p-include-species-labels --p-download-sequences --o-silva-sequences silva-138-sequences.qza --o-silva-taxonomy silva-138-taxonomy.qza

The problem I face here is, filter-seqs-length-by-taxon does not accept silva-138-sequences.qza due to it is a FeatureData[RNASequence]. Expected artifact type is FeatureData[Sequence].

I have skipped cull-seqs step, because I have thought it would take less time if I discarded sequences first. I think that causes this error, seems like cull-seqs changes the artifact type after culling.

If I'm not mistaken, filter-seqs-length-by-taxon should accept FeatureData[RNASequence] artifacts, since it just filters by length not the type of sequence.

Could you inform me where my thought process goes wrong?

And also, thank you all for such a plugin. It helps a lot.

[Nicholas_Bokulich]

Hi @the_dummy,
Very glad to hear you are using RESCRIPt!

@the_dummy

The problem I face here is, filter-seqs-length-by-taxon does not accept silva-138-sequences.qza due to it is a FeatureData[RNASequence]. Expected artifact type is FeatureData[Sequence].

See the following function:

$ qiime rescript reverse-transcribe --help
Usage: qiime rescript reverse-transcribe [OPTIONS]

  Reverse transcribe RNA to DNA sequences.

Inputs:
  --i-rna-sequences ARTIFACT FeatureData[RNASequence]
                       RNA Sequences to reverse transcribe to DNA.  [required]
Outputs:
  --o-dna-sequences ARTIFACT FeatureData[Sequence]
                       Reverse-transcribed DNA sequences.           [required]
Miscellaneous:
  --output-dir PATH    Output unspecified results to a directory
  --verbose / --quiet  Display verbose output to stdout and/or stderr during
                       execution of this action. Or silence output if
                       execution is successful (silence is golden).
  --citations          Show citations and exit.
  --help               Show this message and exit.

Just use that method to convert your sequences before filtering.

Good luck!