cutadapt.md

The usage

1. About

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

2. Usage

# for nanopore cDNA-PCR:
cutadapt -g TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT -a AGCAATACGTAACTGAACGAAGTACAGGAAAAAAAA -g TTTCTGTTGGTGCTGATATTGCTGCCATTACGGCCGGG -a CCCGGCCGTAATGGCAGCAATATCAGCACCAACAGAAA -a "A{20}" -g "T{20}" -a "T{20}" -g "A{20}"  --error-rate=0.1 --times=2 --poly-a -o cleaned_unmapped.fa ./raw_unmapped.fa

# for sqklsk-114
cutadapt -g TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT -a AGCAATACGTAACTGAACGAAGTACAGGAAAAAAAA -g GCAATACGTAACTGAACGAAGTACAGG -a CCTGTACTTCGTTCAGTTACGTATTGC --error-rate=0.1 --times=2 -o cleaned_unmapped.fa ./raw_unmapped.fa