Quality Scores in illumina reads too low

[tobsecret]

Hi,

sickle always gives me an error when I specify -t illumina, telling me that the quality value of some read does not fall within the correct range for Illumina encoding but I know that this particular dataset was obtained from an illumina machine in 2014. Is there any way of fixing this, any additional parameter that I can specify?

[kdm9]

After about 2012 (Illumina 1.8+) illumina uses sanger quality encoding, so as counter-intuitive as it seems you probably want -t sanger.

See the rather brilliant wiki page for more info: https://en.wikipedia.org/wiki/FASTQ_format

[tobsecret]

Oooh, I'm sorry - I'm kind of new to this. Sickle does also not remove adapters, right (manual says no)?