PLEASE HELP!!!! cutadapt 1.12 paired-end trimming: too many parameters

[Dani]

Hi,

I am trying to run paired end trimming with cutadapt 1.12 so STAR aligner won't complain that the two read files are not the same, but somehow it won't run with the command structure that is given in the manual:
cutadapt -a ADAPTER_FWD -A ADAPTER_REV -o out.1.fastq -p out.2.fastq reads.1.fastq reads.2.fastq

cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC —A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o NS2521_S1_R1noadapt.fastq -p NS2521_S1_R2noadapt.fastq NS2521_S1_R1_001.fastq NS2521_S1_R2_001.fastq

but all I get is "cutadapt: error: Too many parameters." no matter if i have options in there or not
Going crazy - what am I doing wrong???
Thanks,
Danielle

[mastal]

The way your command appears in the post, you have the wrong character for the hyphen in front of the parameter 'A'.

[Dani]

Dang - you are right, it doesn't look different in the terminal, but somehow the formatting in the blog revealed the difference
Thank you!

[GenoMax]

If you copied and pasted the command from a PDF file (or some such) then "-" can get converted to "smart hyphens", which look very similar but are hard to detect. Know this happens on macOS often. I generally turn the "smart" feature off in keyboard preference.

[Dani]

Awesome, thank you!