1_Annotation pre-processing.R Error

[francicco]

Hi,

I'm testing your script on my annotation which is from a butterfly species.

I aligned the data using Cellranger 7. I then executed your first script, and I got the following error.

Loading required package: Rsamtools
Loading required package: AnnotationDbi
[1] 0
Error in validObject(.Object) : invalid class “GAlignments” object: 
    'x@cigar' is not parallel to 'x'
Calls: as ... GAlignments -> new -> initialize -> initialize -> validObject
Execution halted

Is there something I have to change or modify?

Thanks a lot!
Best
Francesco

[PoolLab]

It looks like you don't have the GenomicAlignments package in the environment. I would run the following lines of code and try again:
install.packages("BiocManager")
BiocManager::install("GenomicAlignments")
library("GenomicAlignments")

This should hopefully resolve the error.