Nowadays, is there a good way to convert colorSpace fastq from ABI platform to base space format ?
Or at least, to align them in bam and maybe then you can extract to base space fastq ...
I'm used to work with STAR for alignment but it's not designed to align colorspace fastq(same for bowtie2)...so a recent good alternative would be ? Something well maintained.
I read about CUSHAW3...
Just out if interest, what kind of experiment is this and what is the read length?