kdolan-ont comments

Results 5 comments of


                                            kdolan-ont

Dorado Read Splitting Logic is broken (for RNA2)

I have been looking into this. So far, I have not been able to find any artefacts like this in any of our RNA2 or RNA4 data. Based on what...

Using --trim does not remove any bases

@femiliani I have run some of the data you linked to through dorado version 0.5.2, and I am seeing it trim adapters from approximately 2/3rds of the reads. This is...

Overrepensented short sequences in the PCB114-24 data after dorado trim and pychopper

The `SQK-PCB114-24` sequencing kit is associated in dorado with the PCS primers, so as long as the sequencing-kit field in the input pod5 file is set correctly, running `dorado basecaller`...

Overrepensented short sequences in the PCB114-24 data after dorado trim and pychopper

It also looks like the bits of sequence in your examples above that come before the `TTTGGG` sequence are the UMI tags. I think what is happening is that when...

Overrepensented short sequences in the PCB114-24 data after dorado trim and pychopper

@baozg Yes, I think that should just work. Note that if the `TS` tag is not present, then that will mean that dorado was unable to infer the orientation of...