--rrbs and --emseq parameter and argument usage

[deep-buddingcoder]

Description of feature

Hi, I am not a avid user of github and not sure if this is the right place to ask question about a existing feature usage (but not related to new feature request). So pardon me, if I am wrong.

Experimentally, I have generated a human cancer cell line genomic DNA library (MspI digestion followed by NEB EMseq protocol) for CpG methylation analysis using NGS data.

I have couple of questions related to read trimming by Trim_galore!:

Q1. What is the source information for the selection of parameters and arguments for --emseq flag <--clip_r1 10 --clip_r2 10 --three_prime_clip_r1 10 --three_prime_clip_r2 10>? I am not able to match these with information presented in method section of couple of EMseq related papers published by NEB (PMID: 34140313 and PMID: 33468551).

Q2. If I use --rrbs and --emseq flag, both, which argument will be used by the program Trim_galore!: <three_prime_clip_r1 2 --three_prime_clip_r2 2> for --rrbs flag Or <three_prime_clip_r1 10 --three_prime_clip_r2 10> for --emseq flag?

Let me know, if you need additional information from my end. Thanks Deep