02 | March | 2021 | Roberts Lab

Per this GitHub Issue Steven asked that I take a list of gene names associated with DNA methylation and see if I could extract a list of Panopea generosa (Panopea generosa) gene IDs and corresponding BLAST e-values for each from our P.generosa genome annotation (see Genomic Resources wiki for more info).

Here’s the list of gene names provided:

dnmt1 dnmt3a dnmt3b dnmt3l mbd1 mbd2 mbd3 mbd4 mbd5 mbd6 mecp2 Baz2a Baz2b UHRF1 UHRF2 Kaiso zbtb4 zbtb38b zfp57 klf4 egr1 wt1 ctcf tet1 tet2 tet3

The operations were run in a Jupyter Notebook. All results are available in the notebook, as well as in the RESULTS section below.

Briefly, here’s how the process was run:

Use list of gene names to scan GenSAS Panopea-generosa-vv0.74.a4.gene.gff3
Use list of matches to scan both GenSAS BLAST results files:

Panopea-generosa-vv0.74.a4.5d951a9b74287-blast_functional.tab
Panopea-generosa-vv0.74.a4.5d951bcf45b4b-diamond_functional.tab

Extract e-values for any matches.
Print out tab-delimited table of P.generosa gene IDs, gene names, and both BLAST results e-values, if present.

Jupyter Notebook:

GitHub: 20210226_pgen_methylation_gene_IDs.ipynb
nbviewer: 20210226_pgen_methylation_gene_IDs.ipynb

yoda-tea

With Pubathon 2021 in full swing, I’ve been doing more writing (or at least, staring into the distance thinking about writing, then thinking about the analyses and work that comes before the writing, then panicking…)! My goals this month center around completing initial drafts of the Hawaii and Manchester, and setting myself up for new projects next quarter.

February Goals Recap

Hawaii Gigas Methylation:

Evaluated bismark output using coral methylation workflow!
I wasn’t able to look at the methylation with methylKit, but I’ve investigated a few packages (DSS and ramwas) to test out later
Locate an ATAC-Seq dataset that could be used to practice integrating chromatin information with methylation
Started drafting the manuscript!
Investigated ways to identify SNPs from WGBS data

Gigas Gonad Methylation:

Trimmed samples and evaulated with multiqc
Aligned samples with bismark (but have yet to evaluate the output)
I didn’t make it much farther than bismark!
Made a Google Doc for the manuscript…but there are no words whoops

Virginica Labwork:

Sent DNA and RNA for WGBS and RNA-Seq! I should receive samples at the end of March/beginning of April

ATAC-Seq Labwork:

lol this is where the panicking happened

Other:

Continued working on ocean acidification and reproduction review whenever I had time
Completed my review for Evolutionary Applications (not Molecular Ecology I misspoke)
Watched SICB talks and participated in a live discussion!

March Goals

Some very similar goals to last month, with a few additions.

Hawaii Gigas Methylation:

Align samples to the Roslin genome and compare to previous alignments
Extract SNPs from bisulfite sequencing data with BS-SNPer and EpiDiverse
Compare BS-SNPer and EpiDiverse output and determine which approach is suitable
Complete preliminary assessment of DML with methylKit
Try identifying DML with DSS and ramwas
Compare ramwas and DSS DML output and determine which approach is suitable
Determine genomic location of DML
Identify significantly enriched GOterms associated with DML
Identify methylation islands and non-methylated regions
Locate an ATAC-Seq dataset that could be used to practice integrating chromatin information with methylation
Have a complete initial manuscript

Gigas Gonad Methylation:

Align samples to the Roslin genome and compare to previous alignments
Extract SNPs from bisulfite sequencing data with the method determined from Hawaii samples
Identify DML using methylKit
Determine genomic location of DML
Identify significantly enriched GOterms associated with DML
Identify methylation islands and non-methylated regions
Decide if it’s worth extracting gonad RNA for integrated RNA-Seq and methylation analyses
Have a complete initial manuscript

ATAC-Seq Labwork: