How can I reproduce the results of trimmomatic in fastp?

[jeong2624]

I want to perform WGS analysis using BGI sequence data.

To remove BGI sequence adapters, I used fastp and checked for the presence of the adapter sequence using the grep command (linux).

However, the adapter sequence was still present. In contrast, after running Trimmomatic with the same settings, the adapter sequence was not present.

How can I obtain consistent results?

Please show me how to use the FASTQ files from the test data on the fastp GitHub repository, along with the code.

[orangeSi]

for BGI read, is it PE or SE data? Do your fastp parameter had --detect_adapter_for_pe ?

[jeong2624]

Our data is paired-end (PE) data.In addition, we applied —detect_adapter_for_pe parameter.2024. 10. 16. 11:12, myth ***@***.***> 작성: for BGI read, is it PE or SE data? Do your fastp parameter had --detect_adapter_for_pe ? —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>