\r\n is the line break used in Windows or DOS system. Maybe
cutadapt doesn't support it (I didn't try).
You can use
fastp to cut adapters, which can handle different kinds of line breaks (
You can use fastp to preprocess your Illumina sequencing data (no matter RNASeq / DNASeq, no matter PE/SE). It can trim adapters automatically for both PE and SE data, which means that you don't have to input the adapter sequences.
Besides trimming adapters, this tool also performs quality filtering and other operations to improve your data quality. And most of the features are automated. All you have to do is to install fastp, and run:
fastp -i in.R1.fq.gz -I in.R2.fq.gz -o out.R1.fq.gz -O out.R2.fq.gz
This tool is very fast (written in C++, with multithreading supported), you can get it from: https://github.com/OpenGene/fastp
14 days ago by
chen • 1.2k