Cannot figure out, how to generate Qual file for FASTA sequences imported into Qiime2

[Raima (Raima Sen)]

I am new to QIIME2. I read the importing tutorials however I am a bit lost. I intend to run a fungal diversity analysis with mock dataset. I imported the FASTA sequences as the file "sequences.fna" and converted them to "sequences.qza". Can I process the mockdataset further without QUAL file? if so how?

[llenzi (Luca)]

Hi @Raima,
Welcome in the forum!

Yep, the initial importing is usually one of the challenging one!
Although they are not strictly related to fungal analysis, I would still suggest to start working from the QIIME2 tutorials, then move to the fungal pipeline (which is not very different really ...)
Now, for the importing step, can I ask you what is the origin of the fasta sequences you are trying to import? Are these raw sequence files or already denoised file (I am asking because the name you using let me think something already processed but I may be wrong).
All the examples are working with raw fastq sequence-file pairs, which are containing both sequence and quality information, I think it could be possible to import fasta file as well but is not really documented because it is a bit of an unusual case.

A previous port which may be related to your case, if these are already processed sequences:

Importing FASTA sequences for OTU picking/taxonomy assigning

Awesome, thanks for confirming! Woohoo! No need to merge! Just import the feature table and then run your taxa barplot command (assuming that the feature IDs match between these two files - they should if they came from the same analysis). Taxonomic analysis doesn’t need the observation counts provided by the feature table, which is why you were able to do this taxonomic analysis already with just your rep seqs. You need the feature counts to compute relative …

A previous post to help you importing the sequences file in case they are raw data, is:

Importing FASTA file

Hello. I am new to QIIME, and now I am looking up information about importing FASTA file. I have fasta-qual-mapping files (16S, single-end, these files contain the raw sequence data information and still have primers and barcodes) from Illumina Miseq, and the results are not demultiplexing ones. I would like to follow “Moving Pictures” tutorial and Fecal microbiota transplant (FMT) study tutorial (importing, demultiplexing, sequence quality control with Deblur, merging denoised data, and divers…

Hope it helps,
Luca

In general, what type (and how many) of file do you have for your mock-community sample?

[Raima (Raima Sen)]

Hello Ilenzi,
Thank you so much for your response. I looked into the threads you listed about the same problem. I figured I would use the Fastq.gz files instead of FASTA, because it seemed lesser work. I imported the Fastq.gz files. Right now, however, I am waiting on DADA2 step to complete, I have 19-paired-end samples, and 6.3million reads in total. Hopefully it works fine! Thanks a tonne for your helpful reply!