Marcel Martin

Yes, you can use the `anywhere` adapter-trimming parameter. Just write `-a 'ALONGADAPTOR;anywhere'`. This works: ``` $ echo -e '>r\nADAPTORGGGGGGGGGGGGGGGGGG' | cutadapt -N --quiet -a 'ALONGADAPTOR;anywhere' - >r ``` (The third...

No, sorry, I haven’t prioritized it.

I don’t quite see the advantage of using the same number of fields. You’ll need to distinguish between rows representing adapter matches and rows without anyway. Currently, you would perhaps...

The format is intentional, but you have a point with being able to open the file in Pandas or R. Let’s keep this open for now and I’ll give it...

Interesting, can you elaborate a little bit on why you get this type of data? I just wonder whether it would be worth adding support for this to Cutadapt (no...

@yech1990 Thanks for reporting! I have opened a separate issue (#565) as this needs to be fixed in a different way than the problem that @lokapal has.

Can you use `--info-file` for this? See http://cutadapt.readthedocs.io/en/stable/guide.html#format-of-the-info-file

The info file splits each read into three parts: The part before the adapter, the match itself and the part after it, so you could actually deduce whether the part...

It’s been a while, but I’m just going through old issues to see what to do about them. I still think some kind of customizable info file format is still...

Do I understand correctly that you would like to get two output files, one with the reads that were and one with the reads that were note reverse-complemented? This is...