Sean Bennett

Recently Published

Day 10 and Day 135 analysis
Looked at the combined Day 10 and Day 135 samples, with the inclusion of a time covariate.
Day 145
These are the day 145 runs, with the corrected methylation cutoff logic. Macau was run outside of R-studio, to facilitate running multiple instances concurrently.
Day 10, done correctly
So I noticed that I was inadvertently trimming all methylation counts less than 10, as well as the total counts. I should not have done that. The good news is this nets us 267 DMRs as opposed to 41! The bad news, for some reason it makes MACAU run glacially slow.
Trinity type graphs
Proteome Test
Length test
Where'd my DMRs go?
3x coverage Day 135
5x coverage day 135
7x Coverage Day 135
DMR plots
Day 10 analysis
First Results Pass
bedtools and itv testing
Merge 2
merge test
vcf-merge and vcftools --relatedness
Pseudocode description on how to combine multiple SNP files in to a single merged file, and then generate a relatedness matrix.
Geoduck Analysis, first half
Methyl Extract, one at a time
Running Methyl Extract on a single sample .sam file at a time.
Owl Uploader fail
Geoduck BSMap Run
BSMap for ZR1394 Samples
Proteomics test pt2
Emu RAM Upgrade
Emu Upgrade
TA protocol
Rough protocol outline after meeting with Micah at DNR in Olympia.
PECAN install
Primer Database joins
CpG O/E Forest Plot
CpG O/E plot for Geoduck transcriptome, try 2.
Forest Plot code for Geoduck transcriptome methylation
MethylKit output, test run
Testing R notebook functionality with some Methylkit output from Steven's Oly samples.