Marcel Martin

Ah right, of course the command I gave doesn’t do the normalization that `--revcomp` would do. No promises I will have time to do this anytime soon, and more of...

For each of the commands that you listed, *either* the 5' adapter *or* the 3' adapter is removed from each read (depending on which one matches better) because Cutadapt by...

For exactly the reason you mention (because the read may not be short enough), the second specified sequence is actually optional. So whether a read is considered to be untrimmed...

One idea for fixing this: All read modifications could result in a `Match` object.

When you write the command, remember that there should be no spaces around the three dots, so it should be like `-a AAAA...TTTT` etc. Other than that, this should work,...

Hm, are these primers nested? Or does each read have exactly one of the two primer pairs? Cutadapt removes at most a single adapter from each read (a linked adapter...

Hi, thanks for the report. I see that you have included the `-q` option for quality trimming. Quality trimming is done before adapter removal, so at the time the adapter...

Thanks for the suggestion. I cannot promise that I will implement this, but please leave this issue open for now so I will remember to think about it (it may...

This isn’t really supported well at the moment. I think one option is to provide your 96 barcode sequences as anchored 5' adapters like this: `-G ^N{88}ACGTACGT`. The `N{88}` means...

A note to anyone trying this: The error rate should also be adjusted as long as issue #360 is open.