Error appears when running the BamSlam.R

[JingniHe]

Hi, I am working with Nanopore direct-RNA sequencing and found your tools really useful. However, while I was trying to use your BamSlam script to generate some summaries and figures for the alignments, I came across the error below (I generated the bam file using the exact Minimap2 commands suggested by you).

Do you have any ideas what caused the error below, and how I should fix it? Thank you!

A summary CSV file of your alignments.

Rscript BamSlam.R rna align_reads/Min01_aligned_reads.bam Min01

Error:
Imported bam file
Error in [<-(*tmp*, paste0("nbr", col_names_extract), value = c(514L, :
3661425 rows in value to replace 732285 rows
Execution halted

Rscript BamSlam.R rna align_reads/Min02_aligned_reads.bam Min02

Error:
Imported bam file
Error in [<-(*tmp*, paste0("nbr", col_names_extract), value = c(840L, :
943080 rows in value to replace 188616 rows
Execution halted

I am looking forwards to your respond. Thank you!

[josiegleeson]

Hi, apologies for my delayed reply!

I've been trying to replicate the issue on my end, but I can't seem to yet. Is it possible to share a mini version of one of your BAMs so I can test it better? Maybe a download link?

Thank you