Base Quality Out Of Range For Specifed Quality Type

Question

[akshayb04]

Can anyone provide me guidance to the error I am getting when I try to trim my sequence reads from Miseq.

I am using the following command

$ scythe -a adapter_seq.fasta -o trimmed_read.fastq sequence_read.fastq

the error that is displayed is " Base quality out of range for specifed quality type (3): -11"

Please could some one help me understand the error message and what approches should I proceed with to get the right base quality range.

Answer 1

[akshayb04]

I guess I figured out the issue.

This is Miseq reads and the base quality ranges from 0 - 93 unlike Illumina's older versions which has an ASCII offset of 64, Hence while using scythe for trimming 3'end reads for Miseq reads make sure you use

$ scythe -a adapterseq.fasta -q sanger -o trimmedread.fastq sequence_read.fastq

This will then work. Sorry for the confusion guys

Cheers

Answer 2

[Istvan Albert]

Sounds like the FASTQ encoding is of a different type than that expected by the tool. See if you can change the type of the expected encoding.

[akshayb04]

True. It was the same issue Istvan. Thanks