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