What is -e in trim_galore

Question

[evcon]

I was looking at the default settings for trim_galore! and I don’t know what -e means. From the manual -e <error rate="">

Maximum allowed error rate (no. of errors divided by the length of the matching region) Default: 0.1

I get quality rimming, but I don’t understand what error rate could be

Answer 1

[colin.kern]

That setting is related to the adapter trimming and is passed to the cutadapt program. You can read the details here: https://cutadapt.readthedocs.io/en/stable/guide.html#error-tolerance

It basically allows the program to identify and remove adapters in the sequence even if the adapter sequence isn't matched perfectly, which could happen due to sequencing errors that occurred in the adapter sequence.