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Wed. Oct. 30, Geoduck filtered DMR validation

Visualizing filtered DMRs in IGV DMRs have been filtered for 5x coverage in at least 3/4 samples per experimental group, then further filtered for showing a significant difference in % methylation across experimental groups at an uncorrected ANOVA p.value < 0.1 [Read More]

Wed. Oct. 30, Geoduck DMR functional analysis

Match DMRs to genomic features did bedtools intersect on DMR bed files and new annotation gff file: Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3 bed files: All ambient DMRs Day 10 DMRs Day 135 DMRs Day 145 DMRs jupyter notebook: 20191030_DMR_functional_analysis.ipynb [Read More]

Tues. Oct. 29, Geoduck DMR filtering

Performing group stats on DMRs First need to determine best stats model ANOVA GLM family and link options I picked the results from one set of DMR parameters (MCmax = 10bp) and one comparison (day10 samples) to start with I ran ANOVA and GLM to see what each method identifies... [Read More]