Problems with my Bismark Mapper results

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 :

  1. Maybe my R1 and R2 files are not aligned anymore (in a different order) because of my trimmomatic step ?
  2. 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.

Hello @Emm

Please see our tutorials for help with formatting the reads and custom reference genome fasta in a way that tools can understand.