First, do you really need to work with those Solid reads? It is a defunct platform, with not much software available.
I would advise against converting colorspace to basespace, use a mapper / assembler that can take colorspace reads. For RNAseq, Subread and Subjunc (for spliced alignment) can map colorspace reads.
Due to how colorspace reads are encoded, if you convert a colorspace read with a sequencing error to basespace, the error causes a "frameshift" and all subsequent bases are also wrongly converted - this could affect adversely both mapping and (to a greater extent) de novo assembly. However, if you map in colorspace, sequencing errors can detected - as they can be differentiated from true SNPs - and corrected.
See better explanations at:
A: convert SOLID color space to base-space
modified 6 months ago
6 months ago by
h.mon ♦ 24k