I am working with RNA seq analysis, and using Fastp but the output of Fastp after trimming still not good. Any solution.
It is not easy to say what is happening with your data without more information.
Have you read fastp’s manual? Have you tried other quality-checking tools?
according the FASTQC report, this peak is caused by a region of ambigous base-calls in the GSM1949048_Pt2_D726_2.gz dataset, probably due to sequencing errors.
In order to remove those reads you can reduce the N base limit parameter in fastp.