questions about filtering out reads based on the first 3 bases quality in reads before adaptor trimming

[santataRU]

Hi, All,

I wonder if the Sickle program could filter out reads based on the quality of the first 3 bases? I have a custom barcode of 3 bases in the 5' end of my read (e.g. TAG, GAT etc..), I wonder if Sickle could first check the quality score of the first 3 bases in my reads, and discard the whole reads if any one of the first 3 bases quality score lower than certain criteria (for example lower than ASCII_BASE 33 score 30). After discarding these low quality reads, I then use Sickle to trim 3' adaptors. If I understand right, Sickle can do quality trimming of 5' ends, but not discarding the whole reads based on the quality score of the first few bases on 5' ends.

Regards,
Xiao