Hi, I am very new to bioinformatics and would like to ask what do those positions with no "blue bars" mean? I did not do any trimming of primers or adaptors beforehand. My supervisor told me that I should trim away the positions without the blue bars as they do not have any reads, meaning my left-trim position for the forward reads would be set to position 228. And that the left-trim position for the reverse would be position 156.
I am also confused if there would then be any overlap sequences between the forward and reverse reads? Thank you!
Welcome to the forums! This is a great place to learn about bioinformatics.
The blue bars show the 25th and 57th percentile, a.k.a. the middle quartiles, a.k.a. Q2 and Q3 of the quality scores at that cycle position.
If you hover your mouse over the bar, it shows you the quartiles in the box below.
In this screenshot, I'm hovering over that little quality drop at the start, and the box below tells me the median value (50th) along with the 25th and 75th percentile.
Yeah, that can't be right. A blue bar means it has a 25th and 75th percentile, so there must be reads there. Perhaps they are thinking of another program?
There are many discussions on the forums about where to trim before running DADA2. Have you found them yet? What do they recommend?
