PCA of all data show grouping of samples from different temperatures with subsequent time points. This seems to indicate an interaction effect of time x temperature
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Tues. Dec. 17, DMR pipeline
STEP 1: Bismark alignments
A. Build bismark genome
B. Align FASTQs
C. Sort bam files
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213th Post
stats
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Tues. Nov. 12, Geoduck DMR functional analysis
I realized removing part of the 20191108_combine-filt_allc.sh code (#if the context is CG print the chromosome and position) limited the output to require common sites AND coverage across 3/4 samples.
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Nov. 7-9, Geoduck DMR feature analysis
Generate appropriate background I previously used within-sample DMRs filtered for coverage in 3/4 individuals/group as the background. HOWEVER, these did not include all sites that had the potential to be methylated To create a more inclusive background, I need to look at all CG sites considered prior to determining within-sample...
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