Quality trimming on the 3' end

[royfrancis]

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.

skewer \
-x "dna-adapters_1.fa" \
-y "dna-adapters_2.fa" \
-m pe \
-u \
-n \
-k 6 \
-l 20 \
-t 12 \
-q 28 \
-o "sample" \
$1 $2

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?