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josiegleeson / BamSlam

Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
MIT License
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Error appears when running the BamSlam.R #6

Open JingniHe opened 4 months ago

JingniHe commented 4 months ago

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 commented 4 months ago

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