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Problem with cutadapt --length for paired-end reads #345
I am using cutadapt version 1.18 installed by conda on python 2.7.15. When I run cutadapt to trim the reads to a certain length it trims read 1 but does not trim read 2 accordingly. I checked this using fastqc and this can be observed in the "total written" output. Is my command correct or is there a way to properly reduce the length of my paired-end reads?
Thanks for the report. To get the desired behavior, you should follow the advice given in the note that Cutadapt prints:
You are using
Legacy mode exists for compatibility with very old Cutadapt versions. That it is enabled here is actually a bug that I need to fix. And posssibly I just remove the legacy mode entirely in the next major version. There have been many bug reports like yours where people stumble over this suprising behavior (this is why the warning gets printed nowadays).