kent source tree directories:
I've never used the faToFastq program. The fastqToFa takes arguments
to decide the baseQ score scheme. See usage message below. I haven't
tested the -solexa scoring method option.
fastqToFa - Convert from fastq to fasta format.
fastqToFa [options] in.fastq out.fa
-nameVerify='string' - for multi-line fastq files, 'string' must
match somewhere in the sequence names in order to correctly
identify the next sequence block (e.g.: -nameVerify='Supercontig_')
-qual=file.qual.fa - output quality scores to specifed file
(default: quality scores are ignored)
-qualSizes=qual.sizes - write sizes file for the quality scores
-noErrors - warn only on problems, do not error out
(specify -verbose=3 to see warnings
-solexa - use Solexa/Illumina quality score algorithm
(instead of Phread quality)
-verbose=2 - set warning level to get some stats output during processing
Anton Nekrutenko wrote:
Can you share the code? Which baseQ scaling are you using
(Sanger|Solexa)? SOliD support?
On Jul 21, 2009, at 4:35 PM, Hiram Clawson wrote:
> I've written a fastq parser here.