Bwa And Splicing Junctions
Hello, I know that BWA like Bowtie, cann't align reads across splicing junctions, and that's why I have used TopHat to do so. Currently I am using BWA to align reads and further identify SNPs. I am modeling my strategy to the one published recently by Nat Methods. 2012 Jun;9(6):579-81. This paper outright claims to "map reads to the reference genome and across splice junctions" with BWA. They use a pretty standard command-line for this, "bwa samse -n 4". My question is: Does BWA really map across splicing junctions? Am I missing something here? Thanks, G.
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Instead of citing a paper like so
Nat Methods. 2012 Jun;9(6):579-81, in the future please include a hyperlink to the actual paper itself so you can make our lives easier, like so Nat Methods. 2012 Jun;9(6):579-81.