Low Mapping efficiency

[Marh32]

Hi, Felix.

I'm so sorry to bother you again. I have WGBS data from the same batch for two species (Accel Swift data) and have already trimmed it using the method you suggested, with the following command: trim_galore -j 5 -q 20 --phred33 --fastqc --max_n 3 --stringency 3 --length 36 --paired --clip_r1 10 --clip_r2 15 --three_prime_clip_r1 10 --three_prime_clip_r2 10. However, I noticed that one species has a high mapping efficiency (~70%) with a chromosome-level reference genome, while the other species has only ~20% mapping efficiency, with a reference genome that includes over 30,000 scaffolds. In this situation, what steps can I take to improve the mapping efficiency? should I change the --score_min? Thanks in advance.