Below are links to plain text version of my Evernote Notebook used as my primary lab notebook. Pages are in reverse chronological order with the most recent (June 2013) entries at the top. The live Evernote Notebook is available online. This page is primarily serves as an 'offline' archive.
BiGill GFF downloads
BiGill: Figuring out this Effective CT factor
Enterobacteria phage lambda
BiGill - Gene Specific Methylation (Take 3)
BiGill - Redoing Gene Specific Data
BiGill - Visualizing gene level methylation
Olurida Microsats
Bismark: BiGo
Betty BiGO
Bismark: BiGill
Bismark on Cg Fosmid Scaffold
BiGO - Reproducing data / mapping to whole genome
BiGO- methratio troubleshoot
Fixing MG Bedtools
BiGO - Running Gill methratio through Galaxy wflow
Lifting Coordinates within genome..
QPX - Making a Genome Browser
QPX Revisions
QPX SNPs associated with GO terms
QPX - Consistency….
BIO533 Annotating the QPX Genome (exhaustive gene discovery)
TJGR Tandem Repeats and TEs
iPython notebook testing
CE methratio troubleshoot
qDOD - Use Scenario - GO info
BiGO - Reproducing data / Lambda
TJGR - Oyster Genome (entire) Stats
TJGR RepeatMasker on full genome
BedTools Manual
Ruphi OA Clam qPCR
BiGill - Mapping Reads onto entire Genome
qDOD - Example SQLShare Queries
SQLShare Python uploads
qDOD - Practical SQL Share snippets
BiGO - Quality Assessment
Carmel Ab Assembly Annotation
Testing the Backup
Carmel Ab Assembly
TJGR Mgo Exon Relative RPKM
BIO533 Revisiting RNA-seq QPX seperate treatment
BIO533 - Removing Ribosomal RNA sequences
OlyO SNP - aachange
Abalone RNA-seq
TJGR Using gill expression get interval file for MBD Gill
TJGR mCpG and SNPs
TJGR Clusters and closest mRNA
TODO Relationship with Number of Exons
FISH546/TJGR Module 6 Sperm mCpG counts per gene
TJGR Using gill expression get interval file for MBD Gill
TJGR - Capturing Methylation / AS info for sperm
TODO Relationship with tissue expression RPKM table 14
Ab_Assembly Minia
AltSplice: CLC
AltSplice: TopHat_ SplicingCompass
Ab_Assembly SOAP
Olympia Oyster Transcriptome, ver2
Converting UniProt to KEGG
FISH546 Ichy SNPs
FISH546 Metagenomics
Blasting mCpG cluster regions
TJGR BSMAP Gill MBD on oyster version9_90
TJGR; Determining CDS specific expression
Code Comparison PE BS
CDS/intron intersect
TJGR Running BS PE on Lamda
TJGR Running BS PE on Mitochondria
Make +90 Methfile
Determining Coverage for MBD_BS
TJGR Mgo Tophat
Testing Minia for Assembly
Cookbook for R
Notes from: Data Visualization using R
FISH546 Module 3 - de novo assembly
FISH546 Module 4
Blast2GO tests
FISH546 Module 2
TJGR Pinctada fucata
TJGR Genome Comparisons
BIO533 Revisiting RNA-seq QPX
FISH546 Module 1 / b
UniProtKB Swiss-Prot GOA files
TJGR Creating track from Gil MGon RNA-seq reads
TJGR "Promoter" feature track for genome
TJGR GO slim specific feature tracks
DESeq Gill - MGonad
TJGR PE Gonad BS
PoC
NCBI SRA- Cgigas RNA-seq
TJGS Olurida Soapdenovo
Sigenae Download
Cgigas tag-seq RNA-seq for QC visualization
Herring Hepatic Transcriptome Annotation
TJGS Olurida transcriptome version 2.2 annotation
Cgigas tag-seq Repeat Masker
Cgigas tag-seq CLC de novo
Velvet on node 4
SeaFan: taxonomic representation analysis
TJGS - Olympia oyster transcriptome v2
TJGR BSMAP new data (QC)
TGAGA cg_v0.1.2 - BSMAP
TJGR Mapping BS QC on genome v9
testing methratio on genefish
TJGR BisSNP
TJGR BSMAP - BAM
Cgigas tag-seq novoalign combined
BisSNP
TJGR BSMAP - v.9_M
Cgigas tag-seq hashing
Cgigas tag-seq novoalign
Sigenae and the Oyster Genome gene set comparison
Cgigas tag-seq QC report
Cgigas tag-seq Experiment table
Estrogen biosynthetic process
Response to Estrogen Stimulus
Estrogen signalling
Cgigas tag-seq denovo assembly
Cgigas tag-seq on Sigenae
Changing Local Galaxy Server
Cgigas Proteomics Enrichment
Cgigas Tag Seq
BIO533 QPX Taxonomic Representation
BIO533 QPX value added nonsyn SNP
QPX GOslim PIES
Server
TJGR Gene GO annoation
Manila Clam RNA-seq DESeq
RuphiBase files
Oyster field site Water Quality
OlyO SNP table
TJGR - v9_M Repbase
TJGR - CG motifs
TJGR - CG motifs
TJGR - CpG
TJGR - Tandem Repeats Phobos
TJGR - Splice Site Prediction
TJGR - NuPOP
TJGR - Transcription factors
TJGR GFF Features Summaries
TJGR - Transcription SS Prediction
TJGR - Predicting mC
TJGR - Annotating genes
PNW Species Ortho
BIO533 Paper follow-ups
Protein Analysis
Protein Analysis - Oyster, OA
Cgigas Protein Annotation
TJGR - MBD on v9_M
BIO533 Annotating SNPs denovo
A better oyster protein set model
SeaFan OrthoDB analysis
Bleached Coral Assembly
Clam RAD Genetic Diversity
Hard Clam Revisited AGAIN
Hardclam Analysis Revisited
TGAGA: increasing sequence info
Lake Trout SNP data
LT Enrichment
Lake Trout v4 assembly
Lake Trout v5 assembly
Protein Analysis -2 Complete Proteome
Sigenae Blastp Emma
BIO533 QPX Transcriptome 2fold DAVID Output
BIO533 Blast QPX transcriptome v2.1 (ORF) against SP
BIO533 QPX transcriptome v2 against SP
OlyO Broodstock Data Import
BIO533 Nonsynon SNP detection Transcriptome
BIO533 Annotating the QPX Genome
BIO533 QPX Transcriptome GO Annotation
BIO533 QPX transcriptome v1 against NCBI nt (BLAST)
BIO533 DAVID QPX 2-FOLD DEG (WRONG GENE ID output)
BIO533 QPX CpG
BIO533 Mapping RNA-seq on Genome
OlyO larvae combined transcriptome
BIO533 Annotating Phage hunt assemblies
BIO533 - Mining Pacific Herring Transcriptome Data
BIO533 Annotating the QPX transcriptome
BIO533 lab computer trials
Converting Blast to GFF
BIO533 - Turtle Informatics - Specificity
BIO533 QPX Annotation options
BIO533 Annotating QPX assembly 21280
BIO533 - Turtle Virus Informatics
OlyO GOI targeting
OlyO Analysis
PNW Species comparison
Node2 Blast testing - OlyO / nt
Remote blast RepBase TGAGA v032
RepBase - TGAGA v032
Taxonomic Representations
Abalone (WS-RLO) assembly comparison
Custom Databases for BIO533
Symbolic Link and Dropbox
BIO533 Workflow test
Phobos
Pinto Ab Microsatellite
PNW Supplemental Files
OlyO Microsatellite
PNW SNP table
Pinto Ab SNP supp
Pinto Ab SNP
Pinto Ab - SP; GO annotation
SeaFan cross-species
GO pivot
Pinto Ab- Blast (tabular)
Pinto Ab - Blast
OlyO Analysis Blast
Pinto Ab - Assembly
OlyO Analysis: Repeat
OlyO Analysis CpG Galaxy
OlyO Analysis CpG
OlyO Analysis: Pattern Discovery
OlyO Analysis: SNP
Cluster maintenance
OlyO Analysis: GO
Local Blast
blast instructions
DAVID questions
Seafan Enrichment on DESeq geneset
TGAGA cg_alpha0.3.2 Repeat Masker
Elene Vt annotations (5.1)
Pinto Ab Assembly redux 5.1
TGAGA cg_alpha_v0.3.2 - MITE, inverted repeats
Olympia Oyster consensus
Oly annotation
Colton Collection Map
Pinto Ab Data Analysis
v2 Methylation Genome Wide Comparison - Data prep
Methylation Genome Wide Comparison - Dataset stas
Methylation Genome Wide Comparison - miRNA
Methylation Genome Wide Comparison - Sequence Composition
Methylation Genome Wide Comparison - Transcription factors
Methylation Genome Wide Comparison - Pattern Discovery
Methylation Genome Wide Comparison
TGAGA cg_alpha_v0.3.2 Mapping- 454
NZ_AFWI01000000 :: NCBI/NLM/NIH
Function specific tracks for v032
Comparing SeaFan and Nemostella
In Depth BLAST
TGAGA cg_alpha_v0.3.2 Mapping
NSA talk notes
Genomics Gateway
TGAGA cg_alpha_v0.4.0
Jbrowse
TGAGA cg_alpha_v0.3.2 BSMAP
TGAGA cg_alpha_v0.3.2 Annotation
TGAGA cg_alpha_v0.3.0 software/analysis
TGAGA cg_alpha_v0.3.0 BSMAP
TGAGA cg_alpha_v0.3.2
TGAGA cg_alpha_v0.3.0
TGAGA cg_alpha_v0.3.0 Annotation
TGAGA cg_PREalpha_v0.2.0
TGAGA cg_alpha_v0.1.4
TGAGA cg_alpha_v0.1.3 BSMAP
BSMAP Readme
TGAGA cg_alpha_v0.1.3 Read Mapping
Artemis Manual
TGAGA cg_alpha_v0.1.3 Misc Annotations
TGAGA cg_v0.1.2 Annotation Sigenae
TGAGA cg_prealpha_v0.0.1
TGAGA cg_v0.1.2 Annotation CG
OsHV redux
Validating GFF
cgigas_alpha_v0.2.0
Converting DAVID output for specific gene identification
Modified Blast2gff
TGAGA annotation v0.1.0
Map RNA-seq on v0.1.0 (CLC plugin)
Bismark on cg_v0.1.0
BSMAP on cg_v0.1.0
E2 Recp Genomic Stucture
Annotating working Cg Scaffolds
Mapping MBD on cg_v0.1.0
BSMAP on Cg Fosmid Scaffold (aka cg_v0.1.1)
Mapping MBD on Scaffold20/5k
How to convert BLAST results to GFF - BioStar
GFF (General Feature Format) Specifications Document - Wellcome Trust Sanger Institute
OsHV GO
Annotating Fosmids
Bismark
Vt annotation
Skitch note created in Friday Harbor at 4:10 PM
Manila revigo
Running test SNP tables on Vt
BS_Seq on Sigenae 8
FHL Feeding / DO Experiment
Oyster larvae exposed, revisit
2009 Hansen Salmon Notebook
sockeye9
sockeye8
Sockeye6
Sockeye5
Sockeye4
Sockeye7
Sockeye3
BSMAP de novo annotation
BSMAP v2
BSMAP
Oyster fosmid annotation
Black abalone musings
Exploring New Swiss-Prot GO annotation workflow
S4 Clam genes corresponding to enriched GO terms
S3 Clam Differentially Expressed Genes (DEGs)
S2 Immune related gene table
S1 Hard clam contigs
Server Maintenance
Uploading additional oyster fosmids to server
Oyster Genome sequences
Vt Assemblies
Digital Normalization
Data
Science Online 2012 Day 2
Science Online 2012 Meeting Notes
Abalone short read analysis
Cornell Data import
Hard Drive Inventory
bigfishraid
Haliotis ESTs
Seafan Analysis Vol 6
More Ruphi Hyper geometrics
Uploading Ruphi to SRA
Uploading Oyster data to SRA
Pinto trial
Manila clam revigo
Oyster Larvae Size comparisons
Mani Clams on Ruphi
Ion transporters
Intron structure of H transporter (oyster)
Cg BGI assembly
Hard Clam RNAseq
More hard clam
Clam ID genes within Enriched Set
Clam RNA-seq de novo annoation
Cg VTG predicted intron junctions
SeaFan analysis vol4
Cg fosmid Assembly
Pintos OA Exposure NGS data
NGS cell on SRA data
Assembly Oyster "resequences"
PGS - isoform / genomic search
NGS Project Comparison
Multi-species SRA comparison
Converting SRA files on purplepelican
Seafan analysis vol 5
Converting SRA files (Oyster fosmid)
Oyster SRA genomic data - new release
Dowloading oyster SRA data
AY660003 Primer design
Cg PROPS SNP analysis common reference
Cg mitochondria genome
Cg PROPS more genes
Cg PROPS SNP analysis (separate pops)
Cg PROPS additional analysis
Genomic Structure of Cg Elongation factor
Crosson Abalone Analysis
Coho Vitellogenin assay development
bigfishRAID full
Backup of Elene's wiki notebook
Blast Vibrio consensus
Manila clam analysis
sratoolkit install / file extract
sff-dump
Manila Clam NGS
Abalone DAVID analysis
More Crosson RNA-seq analysis
Raid utility error
MBD on SRA (genomic)
Notes on prelim assembly of Oyster genomic "resequence"
Oyster Methylation in silco
Oyster MBD-Seq enrichment
Oyster MBD revisited again (with v6)
NCBI Blast:Nucleotide Sequence (1404 letters) sptlc-1
Ceramide metabolism blast - follow up
Checking correlation with SNPs and CpG ratio
HSF1 and methylation
Hard Clam Report Notes
Thompson qPCR analysis (from scratch)
Ceramide metabolism
Vibrio SNP analysis
Cluster BootVolume full
BigfishRAID space
Notes on Thompson Oyster paper
Bigfish backup
Aurantiochytrium limacinum 454 data
Sockeye qPCR
Oyster 454 contig analysis
Ceramide pcr analysis
Oyster MBD revisited
HSP protein and gene STATs
Oyster HSP Cu notes
Oyster HSP Cu notes v2
bigfishRAID full
Uploading Clam data to SRA
Checking Clam for Laby Seq
LT454 denovo annotations continued
Oyster
Hard clam RNA-seq
HD Failure
Clam RAD
Sole primers
Seafan RNA-seq volume 3
Notes on Clam RAD data
Seafan RNA-seq Analysis (follow-up/double check)
LT SNP discovery
Clam RAD data
Seafan RNA-seq Analysis workflow
Updating BLAST datbases
SeaFan RNA-Seq analysis #fail
Seafan Analysis Restarted
Note on PROPs paper
LT RNAseq and DAVID testing
LT muscle 454
Ceramide pathway paper notes
LT muscle 454 annotations
MBD Oyster RNA-seq
Combining LT muscle de novo
Cufflinks on Galaxy
Seafan de novo assembly GO annoations
Seafan RNA-seq
Seafan RNAseq pre-post visualize (with GO) SPSS
Seafan RNAseq with GO (all data)
Clam RAD
Lake trout muscle RNA-seq
PGS gene expression Vibrio Exposure
PGS expression Tissue Blot
oyster PGS2
OA oyster data
Hansen Sockeye Sample Notes
Herring SNP annotations
Elene Meeting notes
Server reboot
Herring SNP revisions
Server problem
Clam / PGS meeting notes
Hard Clam RNAseq denovo annotation cont
Hard drive Failure
Galaxy workflow
Harding Coho
Elene NGS Vibrio analysis
RBC RNAseq v4.6
RBC -RNAseq v4.0.3
MBD Meth fraction - total read comparison (GOslim)
Oyster MBD de novo
Prelim Trout lamprey RNAseq
Combined Lake Trout (v1) Blast
v4.6 MBD RNA-seq
Network Speed
Comparing v4.6 RNA-seq
Oyster MBD gene specific
Oyster MBD next
Sigenae oyster v8 downloads
Comparing RNA-seq metrics
Sonia gel pics
NOAA sampling draft
Next step
PGS Lake trout BS plate
Gavery BS plate
Sigenae trout SP annotation with GOslim
Sigenae trout SP annotation with GO
Sigenae Trout SP Annotation
trout / lamprey denovo blast
Sigenae Trout data
LT muscle de novo
Sigenae Trout annotation
Colony PCR Bisulfite and PGS
brief: MBD mapping on Sigenae 8
Consensus from Burge OsHV
Server Admin 10.5 Help: Removing Updates from a Software Update Server
swupd folder - can I delete it?: Apple Support Communities
Library adaptors
CLC NGS cell trout
Trout
Lake Trout libraries
HSP BS cloning plate
HSP PCR Gel #1
Hsp gel
HSP PCR #2
MS-AFLP
Hsp PCR # 1
Hsp gel photo
Daves HSP pcr
Sockeye DNMT1
DNMT1 oyster
PROPS FP004705
PROPS CU994646
PROPS CB617519
HSP70 Metzger Paper
Hofman 2008 calcification genes
PROPS FP008495
PROPS FP004879
PROPS CB617519
PROPS AJ582629
PROPS ES789598
PROPS CU996464
PROPS AM857079
PROPS CU988730
PROPS CU988734
DNMT1 oyster
PROPS AM904566
PROPS AM857078
PROPS AM855874
PROPS AJ422120
PROPS BG467400
PROPS EW778389
Salmon dnmt1
sockeye dnmt1
Joins Between Tables - SQL Database Reference Material
Oyster BAC
Second PGS isoform in oysters
Sptlc1 notes
Removing CLC Database
Running BFX cell on single node
Sockeye BFX (again)
Sockeye galaxy blast
sptlc1 oyster
smase oyster
Abalone notes
DNMT3 salmonidae
SRA toolkit conversion
Burge Conversation about SeaFan and OsHV
Analyzing props ngs data
PROPS NGS
BLAST ec2 amazon
CLC bio: Adding Annotations
BFX cell modified S7 Seafan
BFX s_7 Seafan
BFX Coral s_6 library
MV oyster growth stats
MV Gene Expression Stats
Abalone solid
Coral BFX
Burge Laby Data
DNMT3- Sonia
Pathways
Abalone solid on PCR targets
Sockeye
Methylation Machinery
BFX cell
Reminder: Blast oyster on cell
Herring data SRA
Abalone DEG Blasting
Untitled snapshot note
Untitled snapshot note
MV notes
Abalone Solid data
Test entry
Nanotube notes
Emma OA notes
MV Data notes
HSP70
Milford Stats
Herring SNP
BFX herring
Herring data manipulation
RBC SRA Data prep
Unix Cheat Sheet
T-iso agar
RBC de novo
Herring gene ID
Herring BFX
Bacto agar recipe
New Herring annotation
T-iso
larvae
Herring BFX Cell
brains