Hello. I have a user that needs to use Bowtie 0.12.7 (Yeah, old version. Don't ask.) but the quality score format of our FASTQ files is Sanger / Illumina 1.9.
According to https://en.wikipedia.org/wiki/FASTQ_format#Encoding , Illumina 1.8+ introduces a 41st score (letter "J"). And according to that article:
With that in mind, I see this version of Bowtie defaults to:
So my questions are:
1. Will Bowtie 0.12.7 know how to handle the 41st score (letter "J")?
2. If not, where can I find a command-line version of a FASTQ Groomer, like the one in Galaxy?
I appreciate your help.
According to https://en.wikipedia.org/wiki/FASTQ_format#Encoding , Illumina 1.8+ introduces a 41st score (letter "J"). And according to that article:
various scripts and tools break when they encounter data with quality values larger than 40
Code:
--phred33-quals input quals are Phred+33 (default)
1. Will Bowtie 0.12.7 know how to handle the 41st score (letter "J")?
2. If not, where can I find a command-line version of a FASTQ Groomer, like the one in Galaxy?
I appreciate your help.
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