A spoiled enchilada

I aligned all of my files, and proceeded to deduplication, sorting, and indexing in this Jupyter notebook. All of that was successful!

I was ready to use bismark_methylation_extractor but I ran into an error instead. To run bismark_methylation_extractor, I need to provide the path to my deduplicated — but unsorted — .bam files. The error file says that I need to use unsorted files, but I’m already directing the program to my unsorted files! I posted this issue to figure it out.

Since I’m replicating Steven’s code, the only difference in my work and his is that I used the default –score_min option. However, he replicated my work in this notebook and this notebook, but did not get an error! Thinking everything was peachy, I reran my code and still got the same error!

I am officially stumped and unable to continue these analyses for now. Back to the DNR paper!