Closed connor-morozumi closed 1 year ago
In Illumina two-color chemistries (NexSeq, NovaSeq, MiniSeq, ...) G is the absence of signal. This leads to the high-quality polyG tail issue. See here for a brief discussion: https://www.biostars.org/p/294612/
We haven't built a dedicated polyG tail solution, but the rm.lowcomplex
option in filterAndTrim
can help quite a bit. But it may be worth exploring pre-processing solutions that made specific efforts to combat this error type such as fastp, which could be run prior to entering the dada2 workflow.
Thanks, I will try those out. Cheers
I imagine I am doing something like not removing adapters etc but I am hoping to get some guidance on sequences that come out of
dada()
like this:"CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTTTTTAATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACAGTGTCAGCAGCCGCGGTACTCGAGCCCCTCCACACCCTAACCCTAATTCCCACCACAAATCTCTTACGCTGCCAACCCCAGCGCCGCCTAAGGTTCCTCTGAAGCGCCTCACGTCGGAGGAGATGGCGGTACGTAAAGACCAAGTCTCTGCTACCGTATACTGCAGCGATCTCGTATGCCGTCTTCTGCTTGAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"
What are some reasons Phred scores would be high in these tails? Here's an example:
These are NovaSeq with Fluidigm (16s, Archaea, and ITS1 and ITS2 primer sets) where the samples are soybean leaves.
Any assistance on what I am doing wrong (or even some keywords to google!) would be great thanks!