Hi All:

I am trying to learn to use cut adapt for CLIP-seq during this period. Have downloaded and installed cutadapt using conda.

(cutadaptenv) [caiqi@midway2-login1 eCLIP_HNRNPK_HepG]$ cutadapt --version
2.9

Then I run the command like this:

(cutadaptenv) [caiqi@midway2-login1 eCLIP_HNRNPK_HepG]$ cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG-A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o SRR5112140_1.trimmed1.fastq -p SRR5112140_2.trimmed1.fastq SRR5112140_1.fastq SRR5112140_2.fastq

I got an error which myself can not see why:

Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation.

cutadapt: error: unrecognized arguments: SRR5112140_1.fastq SRR5112140_2.fastq

Thank you very much!

Cai