A new enchilada

(P.S. I think I really want enchiladas now)

After fixing the bismark_methylation_extractor issue, Steven suggested I duplicate my notebook and rerun the analysis on a subset of the data. I created this notebook and started rerunning bismark to align the sequences to the prepared genome. I then deduplicated, sorted, and indexed the .bam files, and extracted methylation calls successfully! I also completed the HTML and Summary Report steps. All outputs from this notebook can be found in this folder.

The next step is to duplicate the notebook I created today, remove the -u argument, and run the commands on the full dataset. I created this notebook and started to run the alignment. I’ll check on it in a few days!