Does anyone know if Illumina adapter sequences have changed for NovaSeq 6000? I tried using the sequences described for HiSeq 2500 / TruSeq for trimming my raw data and it didn't work well for removing adapters. I appreciate if anyone could help me with this, I couldn't find this information from Illumina online.
Adapters are usually library preparation kit-specific, not sequencer specific. What kit did you use to prepare the sequencing library?
Jan Oppelt interesting... libraries were prepared using the kit Illumina total RNA stranded with Ribo Zero Plus, and sequenced with the kit NovaSeq SP.
If this (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/stranded-total-rna-prep.html) is true, the kit is based on TruSeq ligation so I would assume it has regular TruSeq adapters (https://support-docs.illumina.com/SHARE/AdapterSeq/illumina-adapter-sequences.pdf).
How do you know you have adapters in your data and that the trimming didn't work?
Jan Oppelt I had a series of odd behavior and bad parameters after trimming, such as the expected distribution of gc content, overrepresented sequences which are common for complete distinct libraries, and a very poor alignment. I have come to the conclusion that this is probably due to incomplete trimming of adapter sequences. If you have other possible explanations, please let me know. I have performed this same process many times before, using the software Trimmomatic, and never saw anything like this. I think you are right about the TruSeq adapters, maybe I should just proceed to test another software.
Maybe you could try BBDuk? https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ and use the truseq adapters included with it? Or even fastp (https://github.com/OpenGene/fastp)
@João Neves da Rocha sometimes it's the easiest just to get some of the unaligned reads and look at them, maybe even BLAST them. Just see what part BLASTs to your target genome and what doesn't. If the unaligned part is the same for multiple reads you can them look for a matching adapter. If you are familiar with command line tools I would suggest Minion+Swan combo from the Kraken package https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991327/
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