Broodstock histology

Met with Kaitlyn in the am and came up with the following plan for scoring gonad histology:

  1. Females:
    • quantify follicle area
    • quantify egg area
    • calculate egg/follicle ratio
    • calculate follicle/tissue ratio
  2. Males:
    • quantify acini/tissue ratio
    • quantify spermatagonia/spermatid ratio (dark purple to light purple)

Comparing allc DMRs and 5x cov files

  • Steven’s 5x cov files:
    • still unsure about what happened in the strandedness code
    • include bases where MAPQ < 30
  • Allc files generated by methylpy (here):
    • filtered for bases with MAPQ >= 30 (–min-mapq 30 default)
  • Methylkit processBismarkAln default includes a ‘minqual’ filter for MAPQ >= 20
  • Not sure if DMG pipeline includes a MAPQ cutoff


  • whatever files we use to validate our DMRs, DMLs, or DMGs, they must be filtered the same way.
    • Otherwise differences may not be apparent when all reads are included…

Some lit on whether to use a MapQ score threshold or not: