I would like to know if there are any methods that can be used to convert colorspace reads from BAM files generated from colorspace reads on the SOLiD system to nucleotide space?
I am looking to use analyze some data generated a number of years ago using both SOLiD 3 and SOLiD 4 systems for alternative splicing. I currently have the aligned BAM files that were generated using LifeScope software but I do not, however, have the csfastq's. I am hoping to run the data through rMATS, or a similar package, to look at alternative splicing events in two different study groups (case vs control). Are there any such things similar to rMATS that would be better suited to handle colorspace?
Any suggestions/guidance would be greatly appreciated! Thank you