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Wed. Nov. 6, Geoduck DMR Summary and Feature Analysis

Summary of DMRs Within-sample DMRs were called (mox script here: 20191024_DMRfindAllEPI.sh; DMR output files here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20191024/, see files ending in _DMR250bp_MCmax30_cov5x_rms_results_collapsed.tsv) and the total number of DMRs called for each of the following comparisons were: All ambient samples over time: 249 All day 10 samples: 182 All day 135 samples:... [Read More]

Nov. 3-5, Salmon DMR analysis

Find DMRs I updated my DMR analysis by including reads with MAPQ score of >= 20 Using methylpy pipeline, I created allc files mox script here: 20191030_DMRfindMAPQ20_Salmo.sh allc files here: https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/analyses/20191030/ created filtered bam files for QC mox script here: 20191030_DMRfindMAPQ20_SalmoPt2.sh filtered bam files here: https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/analyses/20191030/ ran DMRfind to identify... [Read More]

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]