Multi Sample BamQC
Generateed multi sample BamQC report with this jupyter notebook: https://github.com/shellywanamaker/Shelly_Pgenerosa/blob/master/analyses/MultiBamQC_allEPIsamples.ipynb
report here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/multibamQC/multisampleBamQcReport.html
[Read More]
Wed. Sept. 11, 2019 Geoduck genome paper DMR analysis
Check for overlapping DMRs across comparisons
[Read More]
Mon. Sept. 9, 2019 Geoduck Genome paper
DMR analysis of low pH juveniles
[Read More]
Aug 15 - Sept 9, 2019 Salmon-sea lice BS seq analysis
Sea lice bismark alignments: mox script here: https://gannet.fish.washington.edu/metacarcinus/mox_jobs/20190814_BmrkCalig.sh data here: https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/analyses/20190814_Calig/ bismark summary report shows limited mehtylation as discussed on slack here. This isn’t that surprising as the global DNA methylation ELISA data showed Female 1 only 0.56% methylated and Female 2 3.38% methylated. We had tried WGBS with high-ish...
[Read More]
Fri. Sept. 6, 2019 Pt. Whitney Juvenile Var.low pH experiment
Respirometry Ran 1 respirometry trial with 1 animal/vial; each animal from different silo filling vials (tried something different): filled 2.5qt HD buckets halfway with 20um filtered treatment water (this would probably be better with a vaccuum filtration unit, syringe filtering is pretty terrible) placed 12 vials in 24-well plate (as...
[Read More]