Sowmya Parthiban

Hi Andre, Thank you for your quick and detailed response. I believe this is because I ran minimap2 without setting the splice aware parameter. Will update this thread after rerunning...

hi @callumparr, I'm running into something similar, just wondering if you have a better idea now on your last comment (as in what qualifies as many errors)? thanks.

``` library(bambu) library(BiocFileCache) library(readr) library(sessioninfo) library(dplyr) # gtf.file

thank you, Andre!

Suppose I split the samples by chromosome, and generated read classes for these separately, can I put these chromosome_wise_ read class files together before generating the extended annotation?

I was able to save my extended annotation to a gtf for `quant = FALSE` and `discovery = TRUE`. This is what it looks like when I load it. ```...

Hi, are there any updates on this? thanks!

I am interested in this issue. @javierhow is willing to help.