OpenGene/fastp

How can I reproduce the results of trimmomatic in fastp?

Opened this issue · 2 comments

jeong2624 commented

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 commented

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

jeong2624 commented