Difference between revisions of "FlyBase:Complete list of GBrowse/JBrowse Track Differences"

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= Complete list of Data Tracks in GBrowse, not JBrowse =
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{| class="wikitable" style="text-align: center; color: red; margin: auto;"
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!colspan="1"|Warning
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|-
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|rowspan="1"|Information about GBrowse is only relevant to users of an [http://flybase.org/downloads/archivedata archived] instance of FlyBase earlier than FB2022_05.
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For users working with the current release at [http://flybase.org/ flybase.org], please see our page about [[FlyBase:JBrowse]], the genome viewer that replaced GBrowse.
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|}
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= Data Tracks present in GBrowse but not in JBrowse =
  
 
{|cellpadding=3
 
{|cellpadding=3
 
|-
 
|-
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!style="background: #efefef;"| Basic Tracks
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!style="background: #efefef;"| Gene Predictions
 
|-
 
|-
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|style="white-space: nowrap;"| CDS track
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|style="white-space: nowrap;"| CONTRAST
 
|-
 
|-
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|style="white-space: nowrap;"| Restriction Sites
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!style="background: #efefef;"| Protein Similarity
 
|-
 
|-
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!style="background: #efefef;"| Transcription Start Sites
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|style="white-space: nowrap;"| Similarity to Dmel proteins
 
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|-
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|style="white-space: nowrap;"| RAMPAGE (stage specific)
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|style="white-space: nowrap;"| Similarity to Other proteins
 
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|-
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|style="white-space: nowrap;"| MachiBase
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!style="background: #efefef;"| RNA-Seq
 
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|-
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!style="background: #efefef;"| Mapped Mutations
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|style="white-space: nowrap;"| RNA-Seq Developmental Stages, unstranded (Baylor)
 
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|style="white-space: nowrap;"| Transgenic insertions in stocks (Bloomington, Kyoto, Harvard Medical School)
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|style="white-space: nowrap;"| Configure RNA-Seq view (log2 or linear scaling, tilted or vertical tracks, track spacing, track selection)
 
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|-
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!style="background: #efefef;"| Gene Predictions
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!style="background: #efefef;"| Other Reagents
 
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|-
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|style="white-space: nowrap;"| Gene Predictions (NCBI Gnomon, CONTRAST, PhyloCSF)
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|style="white-space: nowrap;"| BAC clones (Tiling)
 
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|-
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!style="background: #efefef;"| Protein Similarity
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!style="background: #efefef;"| Analysis
 
|-
 
|-
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|style="white-space: nowrap;"| Similarity to Dmel proteins
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|style="white-space: nowrap;"| Restriction Sites
 
|-
 
|-
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|style="white-space: nowrap;"| Similarity to Other proteins
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|}
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<br/>
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= Data Tracks present in JBrowse but not in GBrowse =
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{|cellpadding=3
 
|-
 
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!style="background: #efefef;"| Noncoding Features
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!style="background: #efefef;"| Aligned Evidence
 
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|-
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|style="white-space: nowrap;"| TFBS - mesoderm
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|style="white-space: nowrap;"| proteomic peptides
 
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|style="white-space: nowrap;"| Chromatin Domains
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|style="white-space: nowrap;"| Polyadenylation sites
 
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|style="white-space: nowrap;"| Histone Modifications
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!style="background: #efefef;"| Noncoding Features
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!style="background: #efefef;"| Microarray Features
 
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|style="white-space: nowrap;"| Affymetrix
 
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|-
 
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|style="white-space: nowrap;"| DGRC amplicons
 
 
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!style="background: #efefef;"| RNA-Seq
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|style="white-space: nowrap;"| Putative Brain Enhancers (Janelia GAL4 lines)
 
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|style="white-space: nowrap;"| RNA-Seq Cell lines
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!style="background: #efefef;"| Genome Variation Data
 
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|-
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|style="white-space: nowrap;"| RNA-Seq Treatments/Conditions
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|style="white-space: nowrap;"| DGRP Variants
 
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|style="white-space: nowrap;"| RNA-Seq  by Tissue (digestive system, fat body/salivary, imaginal disc/darcass, CNS, gonads, L3 CNS)
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!style="background: #efefef;"| sgRNA Reagents
 
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|style="white-space: nowrap;"| Small RNA-Seq (tissues, developmental stages, cell lines)
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|style="white-space: nowrap;"| Predicted sgRNA
 
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|style="white-space: nowrap;"| Track identities available in color-coded table
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|style="white-space: nowrap;"| Heidelberg CFD KO sgRNAs (conditional knockout)
 
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|-
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|style="white-space: nowrap;"| Configure RNA-Seq view (log2 or linear scaling, tilted or vertical tracks, track spacing, track selection)
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|style="white-space: nowrap;"| TRiP-OE-flySAM.dCas9 sgRNAs (overexpression)
 
|-
 
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!style="background: #efefef;"| Aberrations
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|style="white-space: nowrap;"| Weizmann KO sgRNAs (knockout)
 
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|style="white-space: nowrap;"| Stock Center Aberrations
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!style="background: #efefef;"| Expression Levels: RNA-Seq
 
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|-
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|style="white-space: nowrap;"| Bloomington Deficiency Kit
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|style="white-space: nowrap;"| SRA aggregated RNA-Seq (Oliver lab)
 
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|-
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!style="background: #efefef;"| Other Reagents
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|style="white-space: nowrap;"| FlyAtlas2 (various tissues)
 
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|style="white-space: nowrap;"| BAC clones (Tiling, Pacman)
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!style="background: #efefef;"| Expression Levels: Small RNA-Seq
 
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|style="white-space: nowrap;"| VDRC Vienna Tiles GAL4 lines
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|style="white-space: nowrap;"| FlyAtlas2 (various tissues)
 
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|-
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|}
 
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<br/>
 

Latest revision as of 17:48, 14 December 2022

Warning
Information about GBrowse is only relevant to users of an archived instance of FlyBase earlier than FB2022_05.

For users working with the current release at flybase.org, please see our page about FlyBase:JBrowse, the genome viewer that replaced GBrowse.


Data Tracks present in GBrowse but not in JBrowse

Gene Predictions
CONTRAST
Protein Similarity
Similarity to Dmel proteins
Similarity to Other proteins
RNA-Seq
RNA-Seq Developmental Stages, unstranded (Baylor)
Configure RNA-Seq view (log2 or linear scaling, tilted or vertical tracks, track spacing, track selection)
Other Reagents
BAC clones (Tiling)
Analysis
Restriction Sites


Data Tracks present in JBrowse but not in GBrowse

Aligned Evidence
proteomic peptides
Polyadenylation sites
Noncoding Features
Putative Brain Enhancers (Janelia GAL4 lines)
Genome Variation Data
DGRP Variants
sgRNA Reagents
Predicted sgRNA
Heidelberg CFD KO sgRNAs (conditional knockout)
TRiP-OE-flySAM.dCas9 sgRNAs (overexpression)
Weizmann KO sgRNAs (knockout)
Expression Levels: RNA-Seq
SRA aggregated RNA-Seq (Oliver lab)
FlyAtlas2 (various tissues)
Expression Levels: Small RNA-Seq
FlyAtlas2 (various tissues)
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