Importing .fna and workflow

[Fra (Francesco)]

Hello everyone,

I have a single .fna file containing 118189 sequences in the following format (examples at the end of the message).

While I managed to import this file using the command:

qiime tools import \
--input-path rep_set.fna \
--output-path qiime2/seq.qza \
--type 'FeatureData[Sequence]'

I am unable to move forward in the analyses. Also, while this file looks like an output of DADA2, the sequences are not merged and have primers.

Do you guys have any recommendations?

Example of a sequence within the .fna file:

New.CleanUp.ReferenceOTU99878 Coral.1.27F_812586
GATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGGGGTTTAGATGAAACCAGAGGATGCTTGCATCCTCTTGTGATTCTAAACCTAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCGTATGCAGGGGGACAACAGTTGGAAACGACTGCTAATACCGCATAAGCGCACAGCTTCGCATGGAGCAGTGTGAAAAGATTTATCGGCATACGATGGACCCGCGTCTGATTAGCTAGTTGGTGAGGTAACGGCCCACCAAGGCGAGGATGAGGAGCCGGCCGGAGAGGGTGAACGGCCACATTGGGACTGAGAAACGGCCCAAACTCCTACGGGAGGCAGCAGTGGGGAATATTGAACAATGGGCGCAAGCCTGATGCAGCAACGCCGCGTGAGTGAAGAAGTATTTCGGTATGTAAAGCTCTATCGGCAGGGAAGAAAGGCCTGAAAGGGAGACGACGGTACCTGACTAAGAAGCCCCGGCTAACTCCGTACCAGCCGCCGCGGTAATAC

Thanks
Francesco

[Fra (Francesco)]

I have also tried to follow this tutorial (Clustering sequences into OTUs using q2-vsearch) with no luck.

[Fra (Francesco)]

maybe @gregcaporaso can give me a hint? Thanks!

[annguyen9724]

you can try this :-?
https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494/11