Zenodo archive:
https://rpubs.com/ocattau/1046332
Repository used for displaying geoduck bioinformatic workflow for final thesis purposes
Clean repository used for research: https://github.com/ocattau/code-for-Pgenerosa/tree/main
- Gather Pgenerosa Transcriptome and blast against NCBI swiss prot
- done
- Annotate Pgenerosa Transcriptome with goslims and goterms
- done
- Seperate goterms into individual columns
- done
- Gather other clam transcriptomes
- Manila Clam (Ruditapes philippinarum)
- Mercenaria Mercenaria (Northern Quahog)
- Run blast of Manila and Mercenaria on Pgenerosa
- Manila on Pgenerosa Pgen_db_Manilla
- Mercenaria on Pgenerosa Pgen_db_Mercenaria
- Pgenerosa on Manila Manilla_db_Pgen
- Pgenerosa on Mercenaria Mercenaria_db_Pgen
- Normalize gene counts by % in geoduck transcriptpome
- for tissue types (ctenidia, gonad, heart etc....)
- for species (Mercenaria, Manila)
- Use Heatmaps as a guide for writing discussion
- make heatmaps
- write discussion
- Run blast of Pgen against other clam genomes
- M. Mercenaria
- M. quadrangularis
- R. philippinarum
- A. marissinica
- S. solida
- Make comparative genome table for geoduck paper
- done
- Comparative gonad genome w/ c. gigas
- download gonad genes from Neilly 2012.
- Run blast against P. generosa genome
- filter by reproductive stage
- make table with go slims attached
- describe results
old Rpubs clean research report: https://rpubs.com/ocattau/1041480
annotated R script: https://rpubs.com/ocattau/1041088