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laurahspencer / DuMOAR

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Re-run WGBS analysis using newest Dungeness genome #6

Open laurahspencer opened 1 year ago

laurahspencer commented 1 year ago

Purpose: report genome-wide CpG methylation for Dungeness crab in manuscript

Find mitochondrial contig in our genome assembly - use that to estimate conversion.

@kristamnichols can you find out if mitochondria is in our assembly?

@mgavery re-run WGBS using new genome

@laurahspencer give Mac access to bisulfite converted dungeness crab genome in my directory on Sedna

laurahspencer commented 1 year ago

@mgavery the bisulfite-converted Dungeness crab genome is in this directory on Sedna: /home/lspencer/references/dungeness/

kristamnichols commented 1 year ago

Note the Cancer magister mtDNA genome is published here: https://www.tandfonline.com/doi/full/10.1080/23802359.2019.1691474 and is in NCBI with accession MN371144.1.

@sr320 I'm going to take you up on your offer to do your version of identifying scaffolds / contigs in the genome that are the mtDNA. The genbank accession for the published mtDNA is above, and the full genome, including unscaffolded contigs, is here: https://drive.google.com/drive/folders/1PoG_AxGf_LrBrIgnz20KzlRiQj2i6krk?usp=share_link. In that genome those with scaffold[NUM] in the fasta names for each sequence are the original 49 in this file: https://drive.google.com/file/d/1OWPXBOy93fXZoxjstoUbkuyupDuW-p1L/view?usp=share_link