browse by category or date or tag

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... [Read More]

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

Summary of DMRs Within-sample DMRs were called (mox script here:; DMR output files here:, 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: allc files here: created filtered bam files for QC mox script here: filtered bam files here: ran DMRfind to identify... [Read More]