I would like to have to bases in any read below quality 28. So I need all reads with bases below 28 to be trimmed from the 3' end till a base where the quality is >=28.
It seems like there is some trimming on the last 5 bases on the 3' end probably from removing 3' adapters. But there are still bases in many reads below quality 28 on the 3' end.
I start with this (showing only pair 1):
I would like to have to bases in any read below quality 28. So I need all reads with bases below 28 to be trimmed from the 3' end till a base where the quality is >=28.
I used the
-q
argument like below.I get this (showing only pair 1):
It seems like there is some trimming on the last 5 bases on the 3' end probably from removing 3' adapters. But there are still bases in many reads below quality 28 on the 3' end.
How do I remove these?