there is some discussion of this in another thread.
i'm considering doing the following for bs-treated reads in colorspace:
+ convert C to T in reference (and for reverse-complement of reference)
+ for reads:
+ use aligner (bowtie/bfast) to do mappings
+ ... do usual stuff to calculate per-base methylation
what's wrong with this approach? or how could it be improved for colorspace? is this valid with a subset of reads, so that i could align some this way and then use, for example SOCS (which is very computationally intensive) for unmapped reads?
thanks for any ideas.
i'm considering doing the following for bs-treated reads in colorspace:
+ convert C to T in reference (and for reverse-complement of reference)
+ for reads:
- convert to nucleotide space
- convert C to T
- convert back to colorspace
- convert C to T
- convert back to colorspace
+ use aligner (bowtie/bfast) to do mappings
+ ... do usual stuff to calculate per-base methylation
what's wrong with this approach? or how could it be improved for colorspace? is this valid with a subset of reads, so that i could align some this way and then use, for example SOCS (which is very computationally intensive) for unmapped reads?
thanks for any ideas.
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