Marcel Martin

Thank you for pointing out `--times`, but I have to correct this: > Otherwise, only the first specified option (-g or -a) will be considered by cutadapt when trimming adapter...

Hi, I just made the necessary changes for providing precompiled wheels for Cutadapt. This means that you won’t have to compile the wheel yourself. The wheels will be available for...

Hi, I’m not sure I understand what format the data is in. Can you describe what exactly is in R1 and R2 or do you have a link? Would it...

Thanks, this is helpful. I will probably not be able to add something like this right now, but let’s leave the issue open as a reminder.

Hi, I agree this would be nice to have, but it’s currently not possible. For the moment, you will have to postprocess your read names. Maybe something like this: ```bash...

Hi, sorry I won’t be able to help much with these questions. > what is the difference between cutadapt and porechop I don’t know as I’m not familiar with porechop....

> I personally feel a `--max-error-rate` flag would be very helpful, as it would also work for variable length reads. Is that the `-e` option in fastq-filter? That would be...

> If, for example I would like to filter out any reads whose low-quality base ratio (base quality less than or equal to 5) is more than 50%. I am...

Hi, thanks for the suggestion. I won’t have time to implement this soon, but it is definitely something to consider. I wonder how one would write this on the command...

This may be easy to overlook, but it [is documented in the section about demultiplexing](https://cutadapt.readthedocs.io/en/stable/guide.html#demultiplexing): > Paired-end demultiplexing always uses the adapter matches of the *first* read to decide where...