Can Bowtie 0.12.7 Handle Sanger / Illumina 1.9 ?

Question

[fire_water]

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. I see this version of Bowtie defaults to:

--phred33-quals    input quals are Phred+33 (default)

My questions are:

1. Since the FASTQ files are using the most recent quality score format, will this version of Bowtie know how to handle that?

2. If not, where can I find a command-line version of a FASTQ Groomer, like the one in Galaxy?

I appreciate your help.

Answer 1

[GenoMax]

You can use reformat.sh from BBMap to do the Q-score conversions.

Sanger Fastq (phred+33) is the standard Q-score format.

[fire_water]

Thank you. Do you recommend I convert the Q-score in this specific case or just feed the FASTQ files directly to Bowtie instead?

[GenoMax]

Since your Q scores are already in Sanger format no need to convert.

[fire_water]

Thanks. My only concern is if Bowtie 0.12.7 encounters a "J" in the quality score, will it know how to convert that? Illumina 1.8+ uses "J" whereas Sanger does not. So not sure what'll happen.

[GenoMax]

You can align and see what happens. I have a feeling it might work. There are not going to be many bases with J scores.
If bowtie encounters an error (and you have to use this older version) then you could set those J values to one level lower.

[fire_water]

Your feeling was correct! Bowtie 0.12.7 handled two test sequences with quality scores set to all Js. Thanks again for your help :)