importing data FASTA format

Hi everyone!

I have received some txt files with sequences of 9 samples, each sample contains only one read and is in fasta format, I will attach files of 2 of the samples so you can understand better.

sample31_R1.fastq (664 Bytes)
sample31_R2.fastq (1.7 KB)
so, my question is if this data can be imported with this format to qiime2, and how can I do it, I tried with manifest file and I have not been able to do it.

Your answers would be of great help, thank you!

Hello!

This is done exactly with manifest file, you may find example at my repo: q2-mOTUs/q2_motus/tests/data/paired at main · motu-tool/q2-mOTUs · GitHub

Check how manifest file is constructed and an import command in import.sh.

Good luck
V

1 Like

Hi Valentyn!, thanks for your reply, I checked the format of your samples and they also have a different format than the ones I attached in my topico, when I tried to import with manifest file, I got error in the format, then looking at my data, which is: >id-sample AATGGGGCCTGAACC... and only that per sample, you say I can still work with that?

greetings and again, thank you

Oh, sorry, I haven't seen your files are FASTA, because they are named as FASTQ.
This is also weird, that "reads" refer to sequences without quality.
Please, let's stick to the naming conventions to make everyone's life easier :slight_smile:

If you are sure that you want to proceed this way to QIIME2, then I suggest following:

  • rename your files accordingly
  • install bbmap from bioconda
  • run script reformat.sh in={SAMPLE}.fasta out={SAMPLE}.fastq
  • import them into QIIME2 as FASTQ's with unknown quality

Cheers
V