I am fairly new to QIIME and other script-based programs, but am learning quickly. I was wondering if it was possible to use a FASTA/QUAL (sequences/barcodes) file to run through the Moving Pictures tutorial. I have a FASTA/QUAL file with an associated mapping Metadata file that was produced by a company called MR DNA, many years ago, and I want to do the analyses with the data the same way it was done in the Moving Pictures tutorial. Is there anyway to do this?
Side Note: I have used QIIME 1 to convert my FASTA/QUAL file into a FASTQ file, but I only have a FASTQ file for the sequences and am lacking one for the barcodes, so I am unable to proceed with the single file in the Moving Pictures tutorial.
Thank you in advance for your time and assistance.
There is no way to use fasta+qual files, but you did the right first step (this is an old format so we don’t really intend to support direct importation of this format)
where are the barcodes?
- inline in the read
Use q2-cutadapt to demultiplex
- in the fastq header lines
use other commands in qiime1 to create a separate barcode (maybe extract_barcodes.py)
- in a separate fasta for which there are no qual scores
make fake qual scores for each barcode sequence.
- you have no barcodes because this is one sample
SampleData[PairedEndSequencesWithQuality] format, which are for demultiplexed data, and proceed with denoising/otu clustering.
If the barcodes are in a different place, let us know.
I went with option 2 and was able to extract the barcodes from the sequences and have created a barcode FASTQ file. I am now able to move forward with the Moving Pictures tutorial with my own data set. Thank you very much!
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