Johannes Debler

`secretome.txt` ``` AlAUS0001_000005-T1 AlAUS0001_000005 note SECRETED:SignalP(1-25) AlAUS0001_000006-T1 AlAUS0001_000006 note SECRETED:SignalP(1-16) AlAUS0001_000019-T1 AlAUS0001_000019 note SECRETED:SignalP(1-28) AlAUS0001_000024-T1 AlAUS0001_000024 note SECRETED:SignalP(1-25) AlAUS0001_000034-T1 AlAUS0001_000034 note SECRETED:SignalP(1-22) AlAUS0001_000037-T1 AlAUS0001_000037 note SECRETED:SignalP(1-26) ``` `signalp.results.txt` ``` #...

OK, installed latest version as per your command above, reran interproscan and annotations step, still same result.

Any chance that can be added? Or maybe an option that does something like 'if Adapter trimmed, also trim the next X bases'. Cheers

Alternatively, I could just crop 60 bp (NA top + barcode) from each end of an untrimmed read with something like [chopper](https://github.com/wdecoster/chopper) before assembly and skip `dorado trim` I suppose.

Hmm, good idea. I'm gonna give that a go. I keep my simplex and duplex fastq files separate anyways so I can extract them from separate bams. Any progress on...

I used your suggestion above, extracting the trimmed simplex reads from the inital bam. Thanks, this works fine. There is still the odd barcode in there, but overall looks much...

SQK-NBD114-24 On Fri, 17 May 2024, 00:47 Joyjit Daw, ***@***.***> wrote: > I still have lots of adapters and barcodes left on mine > > what barcode kit are you...

It is also still leaving lots of barcodes on the reads.... at this point i'm probably just going to hard trim 100 bp off each end instead of relying on...

I just had another read of the main page, am I understanding it correctly that `dorado trim` only trims adapters and primers if I feed i an already demultiplexed fastq...

Thaks @malton-ont. To be honest, I have given up on dorado trim and am now just hard trimming all reads 75 bp from each end. Too often I ended up...