Andre Sim

I am glad the issue is fixed. No need to send these files if the issue was due to version differences because of the dependencies. I will close this now,...

Hi, We havn't tested Bambu on any new PacBio Kinnex data, however we have heard reports of it being used to good success, and Bambu has had no problem using...

Hi, This looks very similar to another issue. See this comment for some troubleshooting/workarounds. https://github.com/GoekeLab/bambu/issues/411#issuecomment-1886138264 I hope this helps you finish running your samples, and if you continue to have...

Hi Kenan, If you are meaning the xgboost warnings, that is fine to ignore. We just need to update the packages and push the changes. We just keep getting distracted...

Hi Miguel, I havn't encountered this error before so unfortunately I cannot give you a direct solution, but I am happy to try and troubleshoot it with you. Would you...

Hi Miguel, Interesting that that function ran smoothly, that suggests the error is elsewhere. Did you use the original bam while running that function? Given it isn't occurring there, I...

Hi Miguel, Thanks for that. The error seems to be happening during the junction identification. I am currently guessing there must be an alignment that breaks an assumption we have...

Hi Miguel, This is very strange indeed. Were you able to send the bam file at all? Given the complexity of this issue it will probably be the quickest way...

Hi Thomas, Bambu currently doesn't autodetect the protocol used so I need to check if you set stranded=TRUE when running Bambu? I also want to ask what the use case...

Hi Sowmya, Could you post the output of metadata(se)$readToTranscriptMaps[[1]]? If you read in the rds_files (with readRDS) does the metadata contain the readNames and readId like in the example below...