kent source tree directories: src/utils/fastqToFa/ and src/utils/faToFastq/ 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. --Hiram fastqToFa - Convert from fastq to fasta format. usage: fastqToFa [options] in.fastq out.fa options: -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:
Hiram:
Can you share the code? Which baseQ scaling are you using (Sanger|Solexa)? SOliD support?
Thanks,
anton
On Jul 21, 2009, at 4:35 PM, Hiram Clawson wrote:
I've written a fastq parser here.