Is there any way to follow a pipeline to analyze bisulfite sequencing data?
I know the alignment is tricky, but I've read some people do it with Bowtie without bisulfite genome conversion but I can't guess how to set the parameters to allow the penalty, as expected, I got 95% unmapped. I've also read about using a peak caller to call methylation "peaks".
Of course this is not the best way to do, but after trying a lot, I'm not able to compile any other software in my computer (windows), I'm bench person. I tried to install bismark, bsmooth... but errors everywhere :(