V4 only DADA2 parameters

Hello!

I looked through some similar posts and could not find exactly what I was looking for in regards to DADA2 truncation length and trimming of V4 region reads.

Background info:

Study includes environmental controls( expecting low reads) and clinical samples
V4 region only sequenced, using 806r and 515f primers
overall observe median good quality with reverse showing high variation throughout sequence length.

unlike V3-V4 or other regions in this dataset I do not see a distinct cutoff and was wanting others opinions or insights.

I am thinking potentially:
--p-trunc-len-f 130 --p-trunc-len-r 135 --p-trim-left-f 0 --p-trim-left-r 10

Thank you!

CPPdemux.qzv (324.4 KB)

Hey @nicolejimenez,
Welcome to the Forum :qiime2: Your demux data looks good. I would trunc at 150 because the quality does not really decrease significantly. Your quality median is well over 30 for the entirety of the sequence. I think trunc at the very end of your sequences. As for the trim, that is typically to remove any barcodes that are still in your sequence. If your barcodes have been removed you do not have to trim.
Hope that helps!
Chloe :turtle:

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Thank you! Yes, it helps immensely!

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