Hi,
I processed my data with DADA2 on qiime2 and I like to subsequently perform a dereplication and clustering step with vsearch. To dereplicate the data, it looks like the sequence data has to be in the ‘SampleData[Sequences]’ format.
I didn’t find a way to go from the DADA2 output format of FeatureData[Sequence] to SampleData[Sequences].
So instead, I exported the DADA2 FeatureData[Sequence] file and then tried to import it as ‘SampleData[Sequences]’. When I tried this I got the below error. Is there a way to get the qiime2 DADA2 output into the qiime vsearch dereplicate-sequence plugin? Thanks!
!qiime tools export \
--input-path rep_merge.qza \
--output-path exported-DADA2_seqs
!qiime tools import \
--input-path exported-DADA2_seqs/dna-sequences.fasta \
--output-path exported-DADA2_seqs/seqs.qza \
--type 'SampleData[Sequences]'
There was a problem importing exported-DADA2_240_seqs/dna-sequences.fasta:
exported-DADA2_240_seqs/dna-sequences.fasta is not a(n) QIIME1DemuxFormat filea[Sequences]
$ head dna-sequences.fasta
>00007fa1e4e48c321a7e8ac66fefb764
TACGGAGGGTGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGCTACTTAAGTCAGATGTGAAAGTCCATGGCTCAACCATGGAAGTGCATTTGAAACTGGGTAGCTTGAGTATCAGA
>00009f8c782556f942f2c23c59ed14c8
GCCATTGATACTGGCGTACTTGAGTACGGACGAGGTAGGCGGAATTTATGGTGTAGCGGTGAAATGCATAGATACCATAAAGAACACCGATAGCGAAGGCAGCTTACTAGACCGTAACTGACGCTCATGC
>0000ef72f9fb70069e941768873a1f83
CACGAACCGTCCAAACGTTATTCGGTATCACTGGGCTTAAAGCGTGCGTAGGCGGCTTGGTAGGTCGGGTGTGAAATCCCACGGCTCAACCGTGGAACTGCGCCCGAAACCCTCAAGCTCGAGGAAGATA
>00015cb0a8036853e41c83406c9c8b9a
TACGGAGGGCGCAAGCGTTACTCGGAATCACTGGGCGTAAAGAGCGTGTAGGCGGATAATTAAGTCAGGAGTGAAATCCTATAGCTCAACTATAGAGCTGCTCTTGAAACTGATTATCTAGAATATGGGAGA
info
!qiime info
System versions
Python version: 3.6.12
QIIME 2 release: 2020.11
QIIME 2 version: 2020.11.1
q2cli version: 2020.11.1
Installed plugins
alignment: 2020.11.1
composition: 2020.11.1
cutadapt: 2020.11.1
dada2: 2020.11.1
deblur: 2020.11.1
demux: 2020.11.1
diversity: 2020.11.1
diversity-lib: 2020.11.1
emperor: 2020.11.1
feature-classifier: 2020.11.1
feature-table: 2020.11.1
fragment-insertion: 2020.11.1
gneiss: 2020.11.1
longitudinal: 2020.11.1
metadata: 2020.11.1
phylogeny: 2020.11.1
quality-control: 2020.11.1
quality-filter: 2020.11.1
sample-classifier: 2020.11.1
taxa: 2020.11.1
types: 2020.11.1
vsearch: 2020.11.1
Application config directory
/home/rosales/miniconda3/envs/qiime2-2020.11/var/q2cli