Andre Sim

Hi Sowmya, The intermediate file looks fine to me too, so seeing that final output is very strange. Are you able to run bambu using the test data with trackReads...

Hi Asher, 1. We do have a draft of a tutorial on how to do this. Just give us a week to polish it up a bit and I will...

Hi Asher, You can find the draft tutorial here. https://github.com/GoekeLab/sg-nex-data/blob/add_fusion_tutorial/docs/SG-NEx_IdentifyingFusionIsoform_tutorial.rmd We still need to make some adjustments as when this was originally written the jaffal output was slightly different, however...

Hi Asher, 1. You can use the output from JAFFAL. The outputs should be the same, I believe this was included in the tutorial to show how it could be...

Hi Vincent, Thanks for your report. This is actually what we would expect, as we designed Bambu to be robust to changes in read depth. Higher read depth can lead...

Hi Asher, Yes this might seem a bit unintuitive but it is expected behavior. For background - We found that during multiple sample analysis as you add more and more...

Hi Asher, 1. Yes as canonical transcripts are used in training the model, and are then effectively in the test set they will tend to have lower NDRs. Also canonical...

Hi Asher, Ahh sorry when I meant an NDR of 0.4 was low I meant that it is abnormally good for a sample, since the lower the number is, the...

Hi Asher, No problems with all the questions, they have been insightful. Regarding this minimum count observation, that is not expected and could be a bug. I will see if...

Hi Asher, Sorry about the wait on this. I have tried looking into this but wasn't able to replicate your observation. I was able to run multiple samples together and...