Aug. 21-26, 2019 Geoduck genome paper-DMRs

Aug. 21 Conference call

paper repo:

Current v074 .gff:

  • 8400 gene list that correspond to 5000 proteins
  • TE gff on genomic resources on github

DMG analysis:

  • doesn’t require same loci; just % methylation across DMGs
  • finds common gene loci that tend to be more methylated
  • Comparisons: see supp tables in manuscript

DML analysis:

  • Steven is working on DMLs to compare loci across bivalves

Strandedness:

  • After running Mac’s code, Hollie’s output goes from 8M in bam to 6M in merge.cov
    • code deletes bottom strand coverage of CG
  • We decided to destrand in all our analyses

Coverage:

  • We decided to use 5x and 10x, and will see which is best after analysis

Global analysis of genome methylation

Describe where is methylation in genome:

DMR calling

Methylpy: Destrand data

Methylkit: adjust stringency

  • I had previously set the methylkit unite function to select common sites in samples if they were in >= 2 samples (1L)

  • I tried 3L to see if that would give less false positive DMRs

  • I also tried the default min.group parameter (requires all samples to show coverage of loci)

DMR caller (script linked) min cov/loci destranded? DMR length (bp) addn’l params # DMRs (output files linked)
Methlkit calculatediffmeth 3x N 1000 unite min.per.group = 1L 3248
Methlkit calculatediffmeth 3x Y 1000 unite min.per.group = 3L 529
Methlkit calculatediffmeth 3x Y 1000 unite min.per.group = NULL 529
Methylpy DMRfind 3x N 1000 3 DMLs/DMR 4
Methylpy DMRfind 3x Y 250 3 DMLs/DMR 0
Methylpy DMRfind 3x N 1000 3 DMLs/DMR; DML = 25bp chunk 46
Methylpy DMRfind 3x Y 250 3 DMLs/DMR; DML = 25bp chunk 59
Methylpy DMRfind 3x Y 1000 3 DMLs/DMR; DML = 25bp chunk 56
Methylpy DMRfind 5x Y 1000 3 DMLs/DMR; DML = 25bp chunk 26
Methylpy DMRfind 5x Y 250 3 DMLs/DMR; DML = 25bp chunk 26

*Methylkit R project here: https://github.com/shellytrigg/Shelly_Pgenerosa/blob/master/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/Get_DMRs_for_SR_v074_alignments.Rproj

IGV Sessions

Some DMRs don’t get called after destranding, even though the DMSs are still there. Why is this? Example = scaffold 6 42570880-42570905

Written on August 21, 2019