Reviewing bismark output

In the midst of my existential dread and ennui, I never reviewed my bismark output! I was able to align samples to the genome, then ran multiqc to get summary statistics. I saved bismark output here, and have HTML reports in this repo.

I then looked at the MultiQC report. For all samples, alignment was around 62-63%, which is consistent with the Hawaii samples! About 25% of the reads for each sample were duplicates that were removed from the alignments. This was greater than the Hawaii samples, but makes sense considering that I was using low-quality DNA from gonad in histology blocks. I noticed that samples 5, 7, and 8 had lower percent duplication than the rest of the samples, which is concerning since those are all from the ambient treatment.

There aren’t any big red flags that I can see in the report, so I’ll move forward with methylKit while also aligning to the new C. gigas genome.

Going forward

1. Align to new C. gigas genome
2. Identify DML with methylKit
3. Identify SNPs in WGBS data
4. Write methods
5. Write results
6. Identify DML
7. Determine if RNA should be extracted
8. Determine if larval DNA/RNA should be extracted