Updated Cg genome for Hawaii samples?

[yaaminiv]

I'm working on a methylation analysis of the Hawaii samples. A year or two ago, I remember saying @sr320 that there is now a new Cg genome, and that I should revise my analysis accordingly (analysis was originally done with the Roslin genome). I think (?) either Steven or @kubu4 may have done the bismark mapping with this new genome.

1. Is there in fact a new Cg genome I should be using? The most recent one listed on the Genomic Resources page is the Roslin genome.
2. Was the bismark mapping completed for these samples using the new Cg genome? If so, where can I find the associated output and lab notebook post(s)?

I've searched through Steven and Sam's lab notebooks and haven't found anything, which makes me think that I've hallucinated the whole thing...

[yaaminiv]

I don't think I was hallucinating at all! Found a bunch of scripts @sr320 created in this folder: https://github.com/RobertsLab/project-oyster-oa/tree/master/code/Haws

They all look like bismark scripts. @sr320 can you confirm which genome was used, and if I should take the output from these bismark runs for methylKit instead?

[kubu4]

Genome for Bismark in https://github.com/RobertsLab/project-oyster-oa/tree/master/code/Haws was genome_folder="/gscratch/scrubbed/yaaminiv/Hawes/data/Cg-genome/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/"

[kubu4]

Newest genome is here (Dec. 2023):

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_963853765.1/

Thanks for pointing out that we don't have it listed in the Genomic Resources! Wonder if no one's used it yet...

[kubu4]

Aaand, of course I found it after I posted!

Steven has run Bismark on that genome:

https://github.com/RobertsLab/project-oyster-oa/blob/594a171ef0c327716cacfc75bd9359246c26be40/code/Haws/10-bismark-xbMagGiga1.qmd

[kubu4]

MultiQC report corresponding to that Bismark run with the new genome:

https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/project-oyster-oa/analyses/Haws-10/multiqc_report.html

Bismark output:

https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/project-oyster-oa/analyses/Haws-10/

[yaaminiv]

Newest genome is here (Dec. 2023):

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_963853765.1/

associated publication: https://pmc.ncbi.nlm.nih.gov/articles/PMC11267148/

[yaaminiv]

another output folder: https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/project-oyster-oa/analyses/Haws-14/

Edit: output folder with coverage files and bedgraphs