Where is my .qual file?

[Manuela Ramalho]

Hello Qiime community,

I need to upload some community 16S sequencing data to the SRA, which requires demultiplexed FASTQ files for submission.  My data came from an Illumina MiSeq using a paired-end protocol, and raw data are contained in R1 and R2 FASTQ files.  I first joined paired ends, demultiplexed the joined sequences file using split libraries. I got my seqs.fna, but I could not get my .qual file. To turn my fasta sequences to fastq it's necessary, right? Through the make_fastq.py command...
I never submitted any sequence in the SRA.
Could someone help me?

Thanks in advanced!!

All the best,
Manu

[TonyWalters]

Hello Manuela,

I would use the option --store_demultiplexed_fastq with split_libraries_fastq.py, rather than generating .qual files and then converting back to fastq format.

[Manuela Ramalho]

Hello TonyWalters,

Thanks for the answer!!! This help me a lot!!

All the best,
Manu