Dear all, I have run dada2 on my paired end illumina reads (2x300bp) (already demultiplexed by the sequencing center) with the following command: qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --p-trim-left-f 17 --p-trim-left-r 21 --p-trunc-len-f 296 --p-trunc-len-r 220 --o-representa…

Hi @alfanon , Thanks for providing your artifacts! They are very helpful. My initial thoughts are that this may just reflect true biological content and to not really worry about it. But let's take a closer look to be sure. A few additional questions first: Has there been any other type of qualit…

Dear @Mehrbod_Estaki , thanks for your answer. That's also my guess at the moment. The replies to your questions: I have checked that, and the reads I used are the raw reads coming from the Illumina machine, no QC was done by the sequencing facility. It was a 2x300 bp. I was a bit surprised that a…

Hi @alfanon , Thanks for the follow-up. [image] alfanon: I was a bit surprised that a small fraction of reads are shorter than 300 bp A couple of things come to mind though none of them are particularly worrying in my opinion. First, the tail end of the reads (as is expected with Illumina) m…

[image] Mehrbod_Estaki: Overall, I don’t think this is an issue of the DADA2 algorithm, but rather something from your preparation and even then I wouldn’t worry about it and just carry on with your analyses, taking care to filter out those spurious reads. I agree. I think it is unfortunate t…

Thanks a lot @Mehrbod_Estaki and @Nicholas_Bokulich for your suggestions and feedbacks! Your feedbacks confirmed what I suspected, that the high number of chimeras spotted reflects a problem with the way some of my samples were prepared. Just one last thing @Mehrbod_Estaki : you said that you have …

Hi @alfanon , Sorry that was just poor sentence structuring on my part. I didn't mean that I had shorter reads before QC. I meant to say I've experience denoised merged reads from dada2 to be shorter than the expected length, and those turned out to be host contamination. The full discussion to that…

QIIME 2 Forum

Many chimeric reads after dada2, but only in some samples

User Support

dada2

show post in topic

Home
Categories
Guidelines
Terms of Service
Privacy Policy

Powered by Discourse, best viewed with JavaScript enabled