Re-investigating old paired end MiSeq data present as .FASTA and >QUAL

[drmusk (Muhammad Umar)]

Hi all,
I have an old paired end data from 2015 which I previously analyzed using QIIME1. But now I need to re-investigate that on QIIME2 for some reasons.
I have only .FASTA and .QUAL files and can’t ask sequencing core to provide me with R1 R2, since it is to late to ask this.

I am thinking that I can convert .FASTA and .QUAL into single FASTQ using QIIME1 script convert_fastaqual_fastq.py
But then I do not know how can I convert them to R1 and R2. so that I can use them in QIIME2.

[Nicholas_Bokulich]

@drmusk

I am thinking that I can convert .FASTA and .QUAL into single FASTQ using QIIME1 script convert_fastaqual_fastq.py

Yes

@drmusk

But then I do not know how can I convert them to R1 and R2. so that I can use them in QIIME2.

If you only have one FASTA and one QUAL then this sounds like single-end data. If it is pre-joined, then I recommend importing as pre-joined data and denoise with deblur, then proceed as normal.

Good luck!

[drmusk (Muhammad Umar)]

Hi Dr Bokulich
Thanks
"If you only have one FASTA and one QUAL then this sounds like single-end data".
No my sequences are paired end.
If it is pre-joined, then I recommend importing as pre-joined data and denoise with deblur, then proceed as normal.
Can you be please more specific on that.
Which command should I use to import sequences?

[Nicholas_Bokulich]

Have you read through the QIIME 2 tutorials? Please see this tutorial.

Good luck!