I am working with Sureselect methylseq data. Previously we used the whole reference genome for Bismark alignment with mapping efficiency 50%~60%.
Considering most of reads should be around targeted regions in this kit, it should be better to just map to targeted regions in the provided BED file.
Any idea how to build the reference genome base on a BED file with targeted regions? Thanks!
Considering most of reads should be around targeted regions in this kit, it should be better to just map to targeted regions in the provided BED file.
Any idea how to build the reference genome base on a BED file with targeted regions? Thanks!
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