removing adapters based on IDs not sequence

Question

[alirezamomeni707]

I am using cutadapt to remove the adapters from fastq file. in the paper I got the data from it mentioned that they use P5 and P7 adapters. is there any option in cutadapt to remove this adapters without giving the sequence itself?

[h.mon]

I believe cutadapt can't do this, it can only trim using given sequence. You could create variables for each adapter (which you could append to your .bashrc):

P5ADAPT=AACCGGTT
P7ADAPT=TTAAGGCC

cutadapt -a $P5ADAPT -a $P7ADAPT -o output.fastq input.fastq