I have a seqs.fna file that I imported into QIIME2 with
qiime tools import
I have a quality score heatmap so I’d like to get this seqs.qza in demux.qza format so that I can run dada2 or deblur. How do I do this?
Files in .fna (fasta) format can not be imported into demux files because they are not demultiplexed raw sequencing files. Where did the seqs.fna file come from?
I have been given to work on it. So how I can do the denoising step
You can use
vsearch dereplicate-sequences and then one of the clustering methods in the vsearch plugin. Just know that this is not a typical or recommended pipeline--usually raw sequences (with quality information) are passed to dada2 or deblur for denoising.
Thanks, But as I have a heatmap for my quality score and i know from where i want to trim and trunc. Is there a way I can run the dada2 denoise command ?
Not sure what you mean by a quality score heat map, where did it come from (what tool)?. Dada2 is only going to work if your sequences have quality scores. You can open up your
seqs.fna file and look, maybe it got the wrong file extension some how. Otherwise it's just not possible.
It seems like someone did some upstream analysis with your data (hence this quality graph) and there's a misunderstanding as to what type of sequences you now have and what to do with them. I would recommend reaching out to whoever gave you these sequences to clarify expectations and analysis history.
I have a .fna paired end sequence file and I need to do the diversity analysis.
Do you have any further information regarding where this paired end sequence file came from, and what upstream analysis was performed prior to you receiving it? It's difficult for us to advise you on how to move forward without additional information on the actual contents of your data, along with what analysis has been done on it.
These are raw sequence dataset from our lab which we already had verified from the sequencing vendor. We were tracking down our data but unfortunately couldn't find the fastq files.
Unfortunately without the raw sequences the typical denoising pipeline is not possible. The vsearch alternatives I mentioned above are still an option.
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