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.
- Align to new C. gigas genome
- Identify DML with
- Identify SNPs in WGBS data
- Write methods
- Write results
- Identify DML
- Determine if RNA should be extracted
- Determine if larval DNA/RNA should be extracted