Hi !
First of all, I’m very sorry in advance because I don’t have a lot of knowledge in bioinformatics, it’s all new to me. If you have some easy-understanding documentations to suggest me, I’m all ear !
My problem is that I ran a Bismark Mapper on my WGBS samples, and on all of them, I have a mapping efficiency of 0% …
I first trimmed every R1 and R2 files with Trimmomatic (taking out the adaptors, LEADING of 30, TRAILING of 30 and MINLEN of 50), and then I mapped both files on a mitochondrial genome with Bismark Mapper.
I had in mind that :
- Maybe my R1 and R2 files are not aligned anymore (in a different order) because of my trimmomatic step ?
- I had to make a conversion of my reference genome before using it in Bismark Mapper ?
For both of these possibilities, I’m not sure which tools to use to either rearrange my R1 and R2 files (1) or to make a conversion of my reference genome (2).
Would you have any leads for me ?
Thank you for your help.