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Dear Mikkel,
It would be very helpful if the below information from the documentation at least in brief is included for --trimwindows in the help itself. In the existing help the part regarding 5' is not mentioned. "average quality and the quality of the first base in the window is greater than --minquality." will have profound effect especially in cases where --trimwindows is set to 0 to obtain a read-length average based quality filtering.
(https://adapterremoval.readthedocs.io/en/latest/misc.html#window-based-quality-trimming)
Reads are trimmed as follows for a given window size:
The new 5’ is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than --minquality.
The new 3’ is located by sliding the first window right, until the average quality becomes less than or equal to --minquality. The new 3’ is placed at the last base in that window where the quality is greater than or equal to --minquality.
**If no 5’ position could be determined, the read is discarded.**
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