Quality Scores in illumina reads too low

najoshi / sickle

Windowed Adaptive Trimming for fastq files using quality

MIT License

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Quality Scores in illumina reads too low #47

Open tobsecret opened 8 years ago

tobsecret commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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