My Lab Notebook

stats [Read More]

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. [Read More]

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]

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]

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]