I would like to analyse 454 data using QIIME 2, particularly would like to use the denoise-pyro method of DADA2.
I have experience working with MiSeq data but I am still struggling to get going with 454 data that I was given. I have a single .fna and respective .qual file from the sequencing run, and I was wondering if I can get some help about how to import these to QIIME2, in a format that I can use DADA2.
QIIME 2 does not have any methods to handle separate fasta and qual files. You will need to convert to fastq with another program, e.g., this QIIME 1 script.
Thanks @Nicholas_Bokulich. Thats exactly where I got stuck, though I finally managed to work it out by doing the following:
Demultiplexed data in QIIME 1;
Merged resulting .fna and .qual files by
Created a fastq file for each sample
-i 454/region1_fastq/seqs.fastq --file_type fastq
Compressed the fastq files to fastq.gz using gzip
gzip -r *
Finally imported to QIIME2 using “Fastq manifest” format
qiime tools import --type SampleData[SequencesWithQuality] --input-path se-33-manifest --output-path region1-demux.qza --input-format SingleEndFastqManifestPhred33
I was able to run DADA2 denoise-pyro after going through this. I am not sure if this is ideal or not but it worked. I appreciate if you could point out if there is a better way of doing this.
Looks fine to me. Good luck!
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