Hello everyone, I am working with my own Bisulfite data generated as single-end reads. So, when i'm using Bs-seeker2 i'm getting a mapping efficiency of approx 75-80% but at the same time if i'm using Bismark or BSMap aligner the mapping efficiency get down by 30%. I can't understand the why it is happening,. Any help??

Organism : Arabidopsis thaliana

Read Lenght : 75

bismark command: bismark --genome_folder path-to-genome --se  file1.fq  -non_directional --bowtie2 --parallel 4 -N 1 -L 20 -o Mapped/default

Thank you in advance Chandan