where is the quality cutoff for Read 1? (cutadapt)

Hello,

I am using cutadapt tool via Galaxy with paired-end reads. Where is the option of quality cutoff for Read 1?

I put in the “Optional separate quality cutoff for Read 2” option: 20,20
but I only get the quality-trimmed for Read 2… And, in the Read 1 options I can’t find this feature…

Cutadapt (with Galaxy)

Quality-trimmed:               2,219,321 bp (4.6%)
  Read 2:     2,219,321 bp

Cutadapt (via terminal mac with the tool)

Quality-trimmed:               2,913,773 bp (6.0%)
  Read 1:       694,452 bp
  Read 2:     2,219,321 bp

Thank you in advance!

Hi @silviapc

Is this what you are looking for? I’m a bit curious which version of the tool are you using. But more curious if you think this isn’t working correctly with the most current version → Cutadapt Remove adapter sequences from FASTQ/FASTA(Galaxy Version 4.6+galaxy1)

I do see this update to the tool wrapper that involves the parsing of that term. Change log from Nov 2023.

Would you please try again with the current version and let us know what you think? That is loaded at the three UseGalaxy servers. If you are working on a local server, the admins might need to update the tool.

Let us know what you think, thanks! :slight_smile:

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Oh yes, that’s what I was looking for. I had that tab minimised and didn’t see it.
Sorry for the inconvenience and thank you so much for your help!

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