C. virginica methylation analysis update:

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.

Notebook Entry 1 Copying, MD5 checking, and concatenating
Notebook Entry 2 First round of trimming
Notebook Entry 3 Bismark

Multi-QC report on initial trimming attempt.