I would like to give a brief summary of what I want to do:
I received 3 files from the company: _bcSorted.tar.gz, _trimmed.tar.gz, _joined.tar.gz.
I used_joined.tar.gz after unzipping, I picked the fastq.gz files ending with un1- and un2 only and deleted the files ending with joined.fastq.gz.
I prepared the manifest file using Paired end read type, and it was successfully imported. However when I want to move on to the denoising step, I got this quality please see below.
I am now unable to choose --p-trim-left and
--p-trunc-len. Because of the low quality observed.
Do you have any suggestions why the quality is bad Is that because I choose the wrong file?
Those pictures don’t look awesome for quality scores, I would agree. I don’t think I have a recommendation here either, but it does look like some processing has already been done as a lot of your reads are shorter than the rest. I assume
_joined.targ.gz came after
_trimmed.tar.gz in their pipeline.
What is inside of
_bcSorted.tar.gz, I could see that file-name potentially representing “demultiplexed”, so it might have your “raw-er” data.
If so, I would try working from that instead, it probably won’t help with the quality scores, but I would see what DADA2 is able to do with a few different trim-points.
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