isugenomics / dovetail2scngenome Goto Github PK
View Code? Open in Web Editor NEWDovetail2 H. glycines genome analyses -- falcon,falcon-unzip, scaffolding
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Compose report for Thaumatin-like genes in SCN
Need to summarize the numbers in this data. An orthofinder analysis would provide a nice comparative context.
Samples requested
SCN
Globodera
Meloidogyne
B. xylophilus
C. elegans
1-2 animal parasitic nematodes
Collect and archive all Baum data
Restart Expansion Analysis with new SCN genes -- Orthofinder
Update GIF Bio
Gland RNA SRA submission
Add Seriola Dumerili genome to SeriolaDB.org
Write Deseq methods for Gland RNAseq paper
Create GFF3 functional annotation for gene prediction of pseudomolecule SCN genome for JBrowse
Elk Immune System Genomics
Re-review cichlid paper
Bison genome XY restructuring
need to fix the XY in the bison genome, garbage collection of remaining contigs
Investigate Collaborator access to SCNBase
verify that people have access and figure out how to fix it if they do not.
Manual annotation of the SCN genome via webapollo
- check on sam periodically
- Create mikado input assemblies
Address Reviewers Comments for SCN Dovetail genome
Juicebox the new Hudson SCN assemblies
Elk RNA-seq and diff exp
Reply to Elk genome reviewer comments
Resource release for SCN Pseudogenomes
Create gene and repeat table stats scripts for common_scripts
This is in reference to the tables I created for SCN dovetail genome project
Update CV with new publications
Run SNPeff on filtered SCN population snps
Compose a report for SCN feeding tube candidates
- Peruse the literature to get better descriptions of the types of proteins I would be looking for.
Populate SCNBase TN10 JBrowse with new tracks
Tom has requested a few things here.
Particularly he wants the multiple assemblies of the transcriptome data, i.e. stringtie, class2, braker, etc
Also he has requested that I align the other genomes' genes to the TN10 genome for Jbrowse.
Review Bison grant
GIF annual review
Clean up and release SCN Dovetail genome repo
Add Hudson genomes to SCNbase JBrowse/BLAST
- contact researchIT to inquire about password protection
- create the necessary indices for jbrowse.
Redo the small RNA analysis with the new SCN genome
Is mirdeep2 still the standard here?
Compose report of secreted SCN peptidases
Need to summarize the numbers in this data. An orthofinder analysis would provide a nice comparative context.
Samples requested
SCN
Globodera
Meloidogyne
B. xylophilus
C. elegans
1-2 animal parasitic nematodes
review BMC paper
Call snps for SCN genome populations
Run BCFTOOLS for Kheeman
Add Seriola dumerili to serioladb
Run Blobtools on the three new Abalone genomes.
orthofinder for aphid project
Create presentation for Dec 4 NCSRP meeting
Thomas expects that we will need to present something on the genome.
- Explain mishap of gene prediction
- illustrate route to publication, if not submitted by then.
- Plans for the data that has been generated???
Finish Ryan's analysis
Single Cell Stuff
TRANSFER DATA FROM CONDO AND BOX
Box size limits are no longer unlimited, move to google drive
get data off of condo, as it is being decommissioned in 6 months
Evaluate SCN Pacbio methylation data
SCN Dovetail Genome Publication
Review Sam's SHKT paper/notes
Compose report of Secreted SCN allergen/vap like genes
Need to summarize the numbers in this data. An orthofinder analysis would provide a nice comparative context.
Samples requested
SCN
Globodera
Meloidogyne
B. xylophilus
C. elegans
1-2 animal parasitic nematodes
call snps in elk wild and domesticated populations
NCSRP Quarterly report
Submit SCN gland reads to SRA
Evaluate Nanopore Methylation data for TN10
Orthofinder of Elk to identify immune genes
Create a tutorial for Pacbio methylation analysis
This is a dependency on it working for SCN.
Compose report on secreted SCN proteins with FIDO domains
Need to summarize the numbers in this data. An orthofinder analysis would provide a nice comparative context.
Samples requested
SCN
Globodera
Meloidogyne
B. xylophilus
C. elegans
1-2 animal parasitic nematodes
Compose a report for Shikimate-related SCN genes
Need to summarize the numbers in this data. An orthofinder analysis would provide a nice comparative context.
Samples requested
SCN
Globodera
Meloidogyne
B. xylophilus
C. elegans
1-2 animal parasitic nematodes
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