search

sr320 / ceabigr

Workshop on genomic data integration with a emphasis on epigenetic data (FHL 2022)
4 stars 2 forks source link

Compiling genetic data #69

Closed sr320 closed 1 year ago

sr320 commented 1 year ago

add epidiverse to wiki

kubu4 commented 1 year ago

Looking back at EpiDiverse stuff, I've only run the Oly data through EpiDiverse.

With that being said, do you want me to send C.virginica data through the pipeline?

Would it be the data from here (got the link from the repo wiki)?

https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/

sr320 commented 1 year ago

Sorry about that - got confused with ducks..

Yes if you could send C virg data through pipeline that would be great Yes - that is where bismark bams reside.

kubu4 commented 1 year ago

This finished.

Directory is here:

https://gannet.fish.washington.edu/Atumefaciens/20220921-cvir-ceabigr-nextflow-epidiverse-snp/snps/stats/

Clustering is sort of interesting. Samples seperate out by sex, but there appear to be distinct clusters within each sex:

image

kubu4 commented 1 year ago

Probably should have linked the VCFs directory instead:

https://gannet.fish.washington.edu/Atumefaciens/20220921-cvir-ceabigr-nextflow-epidiverse-snp/snps/vcf/

Regardless, I'll get this info added to the wiki.

kubu4 commented 1 year ago

Notebook: https://robertslab.github.io/sams-notebook/2022/09/21/BSseq-SNP-Analysis-Nextflow-EpiDiverse-SNP-Pipeline-for-C.virginica-CEABIGR-BSseq-data.html

Wiki's been updated.