[Bioc-sig-seq] mappable length of a genome

[Cei Abreu-Goodger]

Hello all,

After short-read alignment, one post-processing step might be to 
normalize by the length (e.g. of an individual exon, of all genes, etc). 
This should actually be the mappable length of these portions of the 
genome, not the real length. Mappable length could be defined as the 
number of distinct k-mers that uniquely align in a given portion of the 
genome.

In a previous thread, Simon Andrews mentioned a Bowtie perl wrapper:

https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2009-May/000315.html

I seem to recall another post suggesting using the BSgenome packages for 
a similar purpose...

Perhaps I'm missing something obvious and this functionality is already 
included in one of the many sequencing-related packages out there.

Any thoughts?

Cheers,

Cei