When the stars (and sequences) align

I successfully completed my genome preparation in Bismark yesterday, so I started on my sequence alignment. Based on the Bismark manual and Steven’s lab notebook post, I used the following parameters in my Jupyter notebook:

1. Path to Bismark
2. -u 10,000: Allows me to subset the first 10,000 reads from each input file
3. –nondirectional: See this issue
4. –score_min L,0,-1.2: This was a parameter Steven used to allow for mismatches in alignment
5. –genome + path to the folder with the .fa genome and bisulfite genome directories Bismark prepared earlier
6. Path to sequence files for alignment

The Bismark run was completed for each file, but I did end up with a gunzip error for each of my files:

I’m not entirely sure what this means, so I opened a new issue. Once I fix this gunzip problem, I can move on to the methylation extraction and start to analyze all of the .bam files this alignment step produced!