add gene to plasmid depth comparison

ktmeaton · Mar 1, 2021 · 8ad86bb · 8ad86bb
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diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md
@@ -9,8 +9,11 @@
 1. Hard code target genes into ref locus bed
 1. Move ref locus bed to reference
 1. Create gene by gene coverage.
+1. Analyze both coverage and depth of loci.
+1. Compare gene to plasmid coverage (pla, pPCP1)
 
 ## TO-DO
 
 1. Add locus coverage output to report
 1. Check if multiqc still runs without eager output dir...
+1. Add latvia samples to database!
diff --git a/results/locus_coverage/all/locus_coverage_pPCP1-pla-depth.png b/results/locus_coverage/all/locus_coverage_pPCP1-pla-depth.png
diff --git a/results/locus_coverage/all/locus_coverage_pPCP1-pla-depth.svg b/results/locus_coverage/all/locus_coverage_pPCP1-pla-depth.svg
diff --git a/results/misc/misc_timetree-branch-major.svg → ...cus_coverage/all/locus_coverage_phylo.svg b/results/misc/misc_timetree-branch-major.svg → ...cus_coverage/all/locus_coverage_phylo.svg