Grace’s Notebook: Oysterseed project progress; Data uploaded to PRIDE

Today I officially got an email that the RAW oysterseed data and *.elib search files have successfully been uploaded and published on PRIDE. I have some plans for finishing up this oysterseed project by October 20th, details in post.

PRIDE submission

Sent the submission in for review yesterday afternoon, heard back this morning that it was approved.


I have to include this information in the paper, and a link to it in my data directory.

### Project timeline End date: October 20th
Week of 9/16: PCSGA (no oysterseed work)

Week of 9/23: Send paper to people who haven’t seen it recently (Yaamini, Laura, Shelly) and get feedback

Week of 9/30: Incorporate feedback

Week of 10/7: Send back to them and include Steven and Emma for feedback

Week of 10/14: Finalize paper, clean up repo.

After October 20th: Submit to BioRxiv (also to a journal??)

from Grace’s Lab Notebook

Shelly’s Notebook: Wed. Sept. 11, 2019 Geoduck genome paper DMR analysis

Check for overlapping DMRs across comparisons

Next steps:

  • determine if there are better (more appropriate) parameters to be using when calling DMRs (see section below). Then redo the bedtools closet on DMRfind output if different than current output.

Compare outputs of different DMRfind parameters

Ambient sample DMRfind result files to compare

  1. min-cov = 5; mc-max-dist = 25, min-cluster = 2
  2. min-cov = 5; mc-max-dist = 25, min-cluster = 3
  3. min-cov = 5; mc-max-dist = 50, min-cluster = 3
  4. merged allc; min-cov = 5; mc-max-dist = 25, min-cluster = 3

Bigwig files to load into IGV

Creating bigwig files:

Summary table of comparison:

parameter –min-cluster –mc-max-dist –min-num-dms –dmr-max-dist –min-cov
descr min #samples/group #bp between sites where mCG counts can be summed min #DMS for DMR to be reported max distance signif. sites can be to be included in same DMR min #reads for DMS to be considered #DMRs called
2 25 3 250 5 192
3 25 3 250 5 22
3 50 3 250 5 32
merge all samples/group 25 3 250 5 716

IGV session:

  • Files loaded:
  • RESULTS: Screen%20Shot%202019-09-12%20at%204.03.33%20PM.png
    • DMR.bed files are ordered as follows:
      1. –min-cluster 3, –mc-max 25
      2. –min-cluster 3, –mc-max 50
      3. –min-cluster 2, –mc-max 25
      4. all samples merged per group, –mc-max 25
    • interesting that some chromosomes have no DMRs when all samples are merged
  • Next Steps:
    • visualize with 5x cov. filtered bedgraphs to confirm DMRs are not false positives
    • create .bw files from merged allc files to see how .bw files from individual samples compared to merged sample files.
      • this is to mainly understand what is going on during merging. From what I understand, the allc files are combined and overlapping CpG counts are summed across samles

from shellytrigg

Laura’s Notebook: Analyzing MACAU results, take 3

New and improved with the following:

  • Included a False Discovery Rate correction as per this paper doi:10.3390/genes10050356
  • 2 heat maps created with % methylation:
    1) excluding loci for individual samples where coverage <5x (retained for other samples), and
    2) excluding loci for all samples if any had <5x coverage
  • Barplot of lengths in same order as 2nd heat map

See new RMarkdown notebook: 006-analyzing-MACAU-results-rev1

Preview of new plots


from The Shell Game