Sun. Jan. 30, 2022

Update & Monthly Goals –
Prior Monthly Goals Complete gigas-WGBS-ploidy-desiccation manuscript Submit mussel OA shell repair manuscript to JMSE special issue CICOES Postdoctoral Fellowship application (1/23) Submit RNA samples to UT Austin GSAF Curate master RNA sample list for PSMFC mussel project Get SICB talk up and running Monthly Goals for February Complete gigas-WGBS-ploidy-desiccation manuscript….

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Data Wrangling – C.virginica Gonad RNAseq Transcript Counts Per Gene Per Sample Using Ballgown

As we continue to work on the analysis of impacts of OA on Crassostrea virginica (Eastern oyster) gonads via DNA methylation and RNAseq (GitHub repo), we decided to compare the number of transcripts expressed per gene per sample (GitHub Issue). As it turns out, it was quite the challenge. Ultimately, I wasn’t able to solve it myself, and turned to StackOverflow for a solution. I should’ve just done this at the beginning, as I got a response (and solution) less than five minutes after posting! Regardless, the data wrangling progress (struggle?) was documented in the following GitHub Discussion:

  • [Help with unwiedldy table(https://ift.tt/3KP3yRp)

The final data wrangling was performed using R and documented in this R Markdown file:


RESULTS

Output file (CSV):

Ultimately, the solution came down to this tiny bit of code (see the R Markdown file linked above for actual info about it):

whole_tx_table %>%
select(starts_with(c("gene_name", "FPKM"))) %>%
group_by(gene_name) %>%
summarise((across(everything(), ~sum(. > 0))))

That’s it!

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January 2022 Goals

image

Break? Over. Rest? Acquired. Projects? Ready to be tackled.

Me? Not ready to work yet but oh well here we go.

I have some lofty goals this month, but my plan is to try and split my time more effectively between my PhD and postdoc projects. I think I’ll work a couple days at home and dedicate those to PhD projects, and spend my office days working on postdoc projects. Hopefully the physical separation will help me compartmentalize the work so I don’t feel guilty for not working on postdoc projects while working on my PhD projects, and vice versa!

November Goals Recap

Gigas Gonad Methylation:

  • SO CLOSE to finishing reworking the discussion! But also not done. Whoops.

Hawaii Gigas Methylation:

  • I didn’t have time to work on the Hawaii paper, but now that I have Rajan’s feedback I can start to incorporate that as I restart my work

Virginica Gonad Methylation:

  • Talked through methods with Steven and Sam
  • Have yet to extract SNPs or perform any actual analysis myself

Coral Transcriptomics:

NSF PRFB:

  • Successfully wrote and submitted my NSF PRFB!

Other:

  • Finished identifying new papers for ocean acidification and reproduction review
  • Completed Molecular Ecology review
  • Identified a killifish RRBS and RNA-Seq dataset to work on with Neel
  • Discussed potential projects involving DNMT-3 knockout zebrafish or menhaden with Neel

January Goals

Gigas Gonad Methylation:

  • FINALLY finish the discussion
  • Revise the introduction and abstract
  • Send to Steven for edits
  • Submit to a journal and bioRXiv

Hawaii Gigas Methylation:

  • Address Rajan’s edits
  • Review DSS script and determine if I should go back to methylKit for better interpretation
  • Extract SNPs with EpiDiverse and create a relatedness matrix
  • Look at methylation islands and non-methylated regions
  • Examine overlaps between DML and other epigenomic datasets from Sascha

Virginica Gonad Methylation:

  • Update methods of draft paper
  • Extract SNPs with BSnper and EpiDiverse
  • Identify methods for linking WGBS and RNA-Seq data
  • Identify lncRNA and miRNAs in dataset

Coral Transcriptomics:

  • Continue testing extraction protocol to identify a successful methods
  • Use gel to check RNA integrity
  • Extract all A. cervicornis samples

Killifish Methylation and Expression:

  • Review BAT mapping and DMR identification protocol
  • Start mapping procedure for methylation data
  • Identify protocol for RNA-Seq data

Ocean Acidification and Reproduction Review:

  • Start integrating new papers into main text and supplemental material
  • Revise figures

Other:

  • Meet with Carolyn, Ann, and Neel to discuss projects and funding opportunities for the next six months
  • Develop any potential projects
  • Coordinate postdoctoral mentoring program with Maggi

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