I re-ran the data files through a different trimming program, Trimmomatic, with a specified Illumina TruSeq adapter set and got better results from FastQC. Running things through Bismark once more, and we’ll see if we get better mapping rates that way. Tomorrow I’ll likely run stuff through BSMap as well to see if I can match, or beat the ~20% rate Steven got comparing to the gigas genome.
I ran Bismark on the oil exposed C. virginica samples from LSU over the weekend and got pretty abysmal mapping rates, between 4% and 8% terrible. I looked through the quality data and noted that there was some oddities in one of the samples with residual TruSeq adapters post trimming.
I talked to Sam and he remembered that this was an issue with this data the last time it was looked at, so we decided to re-try the trimming function, specifying TruSeq adapters, as well as trimming the first 5 sequences due to relatively lower quality.
Multi-QC report on initial trimming attempt.