Wed. Sept 26, 2018

My goals for today

  • Work on Bismark alignments
    • Trying different alignment score settings:
      • Looked into bowtie2 alignment manual
      • alignement score is dependent on matches and mismatches
        • alignment score of 0 = 100% perfect match
        • 1 mismatch = -6 score
        • 1 ambinguous character = 1
        • if there’s a gap in the reference seq. or the read seq: 5 + 3*gap length
          • a 2bp gap in the read seq. = 2 insertions (relative to the read seq.)
          • a 2bp gap in the ref. seq. = 2 deletions (relative to the read seq.)
      • default in normal alignment mode is L, 0, -0.2 (where L = linear, the first number = the intercept, and the last number = the slope, and x = read length). The default specifies for reads that are 100bp the alignment score must be >= -20.
        • in –local alignment mode, G is used and G = natural log (i.e. f(x) = 1.0 + 5.4ln(x), where x is the length of the read). The min score default in local mode is 26 for 100 bp read.
    • my old alignment settings for the CrY2H-seq pipeline were:
      • –local mode
      • mismatch <= 2
      • indels <= 2
      • 30bp match length
      • no softclipping in the beginning of a read because that is where the quality should be the best
    • Compare different alignment score thresholds (i.e.-0.6, -1.2, etc.)
      • look at % aligned
      • run dedup.
  • Caught up with Brent (brentv@uw.edu)
    • set up meeting time with Steven and Brent (Monday Oct.1 @ 1:30)
    • Pt. Whitney can bring in 80 total animals
    • possible conditions could include
      • an acute low treatment (i.e. pH shock for 1 month)
      • different collection times to expose different stages of gonad dev.
    • need to do a power analysis to see # animals needed and # of possible treatments
    • how to infuse CO2 in seawater tanks?
      • venturi injector in intake line?
      • find out it’s done in MOATS


Written on September 26, 2018