BerrocalRubio333

Hi Andre, Thank you for your very fast and kind response. I have run the original bam, which gave me the error. What I have done them is filter certain...

Hi Andre, Yes I am running the bam with all the chromosomes. This was the mapping: minimap2 -t 10 -2 -ax splice -uf -k 15 --MD --junc-bed ~/tools/minimap2-2.26_x64-linux/reference/human/gencode.v39.annotation.bed --secondary=no ~/tools/minimap2-2.26_x64-linux/reference/human/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta...

Hi Andre, You are correct, the location is always in a junction, normally from what I have seen in the most 3' exon of the read (not sure if that...

Hi Andre, happy to send you a bam with one of the chromosomes that give me trouble so we can try and troubleshoot it there. Would you let me know...

Hi Andre, it seems like the error was coming from a problem with the versions of co-dependent packages. I solved the problem by creating a new environment from scratch, and...