FastQ ColorSpace to BaseSpace format in 2018

Question

[ZheFrench]

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...

[ATpoint]

Just out if interest, what kind of experiment is this and what is the read length?

Answer 1

[Antonio R. Franco]

You cannot convert colorSpace to base format. One incorrect color/transition will propagate such that all the remaining bases will be incorrect upon conversion.

Old versions of Tophat still can map solid sequences. You are running out of alternatives

Answer 2

[h.mon]

It will be difficult to find "Something well maintained" that maps a nearly defunct sequencing technology. Surprisingly, there is a very good DNAseq and RNAseq mapper capable of dealing with colorspace reads: Subread. The only caveat is I never used it on colorspace reads, only basespace reads - with good results - so I really can't say if it does a good job or not for SOLiD reads.

Do you have RNAseq or DNAseq? I have used CUSHAW3 for colorspace reads, and it did a good job, but I think it only does unspliced alignments.