Hi! I had went to view my demux.qzv file and this is the quality plot that I was given. I haven't seen one that looks like this before. I was wondering if it looked ok and where it would be plausible to truncate since there doesn't seem to be a clear point where all of the data starts to lose quality. I have attached the image below. Thank you in advance!
What kind of sequencing platform is your data from? My first guess is this is the result of binned quality scores from the Novaseq or Nextseq.
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Yes, the samples weresequenced in a NovaSeq 6000 SP lane with 2x250nt and produced ~ 1 billion reads.
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HI again @Nadine_Veasley ,
I believe you have your answer 
. These plots are due to the sequencing platform you used, they give binned quality scores - so the quality plot looks different.
Try searching the forum (it's an amazing resource if you tap into it!) . There are many posts on the forum about moving forward with this data, like this one.
best,
Vic
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