Hi,so I am working with 30 samples of 16s and they have this primers 341f/785r.I have demultiplexed them and I tried to use “cutadapt trim-paired” to remove the primers,another guy had worked with this before but he is not in the lab anymore,so I saw he wrote this Reads were trimmed the foward and reverse primer minimum length: 402 pb; maximun length: 429; minimum quality score: 25; degree of mismatching allowed: 0; homopolymers no longer than 10. Reads with ambiguous bases and singletons were removed. Chimera were checked and removed from the dataset with the consensus method. 1
I tried setting this parameters in galaxy but den I use demux summarize and i have 0 of everything,also how do I use qiime dada2 denoise-paired if I put the minimum lenth in the cutdap?thank you
It looks like data/job setting issue. The best option is to get an advice from ppl in the field.
Do you work with long reads (PacBio, Nanopore)? If yes, do you use the same sequencing platform as the “another guy”? Have you done QC for the reads? How the results compare with settings used in the filtering step? For example, Nanopore reads most likely have quality score below 25.
Maybe check tutorials in:
Kind regards,
Igor
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