Mapping In Colorspace

Question

[Frenkiboy]

I tried mapping my data both in letter and color space and the results look markedly different.

Multimapping is much more pronounced in the color space mode.

Does anybody know why this is happening?

(Bowtie and Shrimp were used for mapping)

Tnx!

[GAO Yang]

Your reads are color-space; and you tried Way 1: reformat reference-> color space ; map the reads to color-space reference；Way 2：reformat reads->base; map reads to base-space reference. Am I right?

[Frenkiboy]

I have changed my question a bit. You are correct about the methodology. The thing that's been bugging me is that the reads in colorspace have multimap to many more locations.

Answer 1

[Ketil]

Converting colorspace reads to base-space, any error introduced will dramatically change the remaining sequence. So it's to be expected that the mappings will be different. If you map directly in colorspace, the mapping may take this into account. Mapping reads with (assumed) errors will then produce multiple mappings, but in general multiple mappings is a function of mapping stringency - you can likely tune your aligner to give more dubious alignments in base-space as well if that's what you want :-)