TopHat 2.0.4 prep_reads Error

[Dario1984]

According to FastQC, I have data with Sanger / Illumina 1.9 quality encoding. But, I get an error with TopHat using --solexa1.3-quals. The log file says

Saw ASCII character 63 but expected 64-based Phred qual.
Try not specifying --solexa1.3-quals/--phred64-quals

But the TopHat manual instructs to "Use this option for FASTQ files from pipeline 1.3 or later."

[Rachel Hillmer]

I think that's an error in the TopHat manual. From CASAVA v.1.8 and forward in time, Illumina now reports Sanger quality scores. The option you describe is valid for illumina pipelines 1.3 up to but not including 1.8.

http://en.wikipedia.org/wiki/FASTQ_format#Encoding