repository for FISH 546 homeowork and assignments see https://github.com/ocattau/code-for-Pgenerosa/tree/main for research progress and https://rpubs.com/ocattau/1046332
Week 1 - presented research at National Shellfish Association Meeting
Week 2 - Got COVID, started downloading clam transcriptomes
Week 3 - gather genes from each tissue type, build sh files for blasting manilla clam and mercenaria against pgen in Mox, Run stand blasts with Manilla, Pgen and Mercenaria build database for Manilla, Pgen and Mercenaria, start writing methods
Week 4 - dowload to raven the genomic and transctiptomic information for 6 clam species, find transcriptomes for introduction, break goslims into seperate columns, join blast tables with annotation tables
Week 5 - added new normalizing gene count column for heatmapping, finished writing draft 1 of results, working on methods, finish introduction
Week 6 - finish writing introduction/discussion for geoduck paper
Week 7 - address edits from Steven for CS work, run blast against other clam transcriptomes (step 8), make table for compairative clam analysis, update methods and results in geoduck paper
Week 8 - download Dheilly 2012 data and analyze
Week 9 - Zenodo archive, clean repos, address Steven's edits for geoduck work
Week 10 - finish edits for discussion and results for geoduck chapter -- make final repo clean
- 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