adrc2015 gbrowse2 min - flybase · release&5®ion* release&6&coordinates&...
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New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-‐Seq data, and more
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Hoskins, et al. (2015). Genome Res. [Epub ahead of print] (PMID: 25589440)
• Improvement to centric heterochromaRn regions.
• Improved Y chromosome assembly (now 10 Rmes larger).
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0 Mb 5 10 15 20 25 30
r6 X r5 X r5 XHet (100%)
Release 5 -‐ Release 6 comparison
r6 Y r6 4 r5 4 r5 YHet (67%)
r6 2L r5 2L r5 2LHet (93%)
DepicRon approximates NCBI Release 5-‐to-‐Release 6 Alignment
r6 2R r5 2R r5 2RHet (71%)
r6 3L r5 3L r5 3LHet (90%)
r6 3R r5 3R r5 3RHet (90%)
*% of r5 ‘Het’ mapped to r6 arm assembly indicated.
*
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Release 5 region* Release 6 coordinates size (Mb) shia (bp) X:4,684,795..20,073,489 X:4,790,762..20,179,456 15.4 105,967 2L:1..21,485,538 2L:1..21,485,538 21.4 0 2R:3,037..16,668,212 2R:4,115,532..20,780,707 16.7 4,112,495 3L:5,114,766..24,523,740 3L:5,121,666..24,530,640 24.5 6,900 3R:1..27,905,053 3R:4,174,279..32,079,331 27.9 4,174,278 4:24,054..1,221,288 4:3,428..1,200,662 1.2 20,626
*For each Release 6 chromosome arm assembly, the largest region of uninterrupted idenRty from Release 5 is shown. A complete liaover table is available at h>p://flybase.org/reports/FBrf0225389.html
Most feature coordinates have changed.
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Mapping of Release 5 sequences to Release 6: pseudoscaffold U is no more
• 24% of r5 U sequence has moved onto the r6 chromosome arm assemblies: • X_ – 223 kb • 2L – 40 kb • 2R – 994 kb • 3L – 150 kb • 3R – 1,027 kb
• 1,862 minor scaffolds remain as disRnct enRRes (not a pseudoscaffold).
• About half of the minor scaffolds have been mapped cytologically: • e.g., 2CEN, 3CEN, rDNA, Y.
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MigraQon of FlyBase features to Release 6
• The vast majority of FlyBase features migrated automaRcally, using mapping table derived from NCBI genome alignment.
• 77 gene models required manual review. • 31 gene models were deleted (non-‐coding repeats) • 13 gene models had protein coding changes. • 33 mapped to the new assembly without major changes.
• 11 new gene models were assembled from 40 annotaRon fragments due to improvements in centric heterochromaRn.
See the current release notes for full details of affected genes. h>p://flybase.org/staQc_pages/docs/release_notes.html
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MigraQon of FlyBase evidence to Release 6
• NCBI has provided new alignments of nucleoRde and protein sequences.
• Sue Celniker’s group has provided modENCODE RNA-‐Seq data newly mapped to the Release 6 assembly.
• Other RNA-‐Seq data has been migrated by FlyBase.
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Access to Release 5 data: FlyBase Archives
h>p://flybase.org/staQc_pages/downloads/archivedata3.html
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Access to Release 5 data: FlyBase Archives
h>p://flybase.org/staQc_pages/downloads/archivedata3.html
GBrowse
BLAST
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Access to Release 5 data: FlyBase FTP site
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Coordinates Conversion: FlyBase converter
h>p://flybase.org/staQc_pages/downloads/COORD.html
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Coordinates Conversion: NCBI remap tool h>p://www.ncbi.nlm.nih.gov/genome/tools/remap#
*The Release 6 “plus MT” and “plus ISO1 MT” differ only in the mitochondrial genome.
*
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FlyBase policy: migraQon of new data to Release 6
• For a limited Rme, FlyBase will accept Release 5-‐based data and lia it over to Release 6.
• FlyBase will replace any FlyBase-‐migrated dataset with a new analysis directly mapped to the Release 6 genome assembly.
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Be mindful of the reference assembly in use Dmel Release 6 genome assembly
4th gene model annotaQon version on this assembly
FlyBase version
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Release notes h>p://flybase.org/staQc_pages/docs/release_notes.html • General FlyBase staRsRcs.
• Detailed informaRon about the reference genome assembly in use for each species.
• Summary staRsRcs on gene model annotaRons and other annotated features.
Be mindful of the reference assembly in use
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• Specify the reference assembly and FlyBase annotaRon version used in your publicaRons.
• Check the reference assembly and annotaRon version in use at other databases, resources and datasets.
Be mindful of the reference assembly in use
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• GBrowse 2 was developed by the Generic Model Organism Database (GMOD), and integrates nicely with GMOD tools.
• GBrowse 2 (2010) replaces GBrowse (2002).
• FlyBase has offered GBrowse 2 (beta) since March 2013.
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GBrowse 2 handles more data • Display of quanRtaRve (wiggle) tracks and next-‐generaRon sequencing (NGS) data.
• Ability to display all tracks in a single view.
è è è
è
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GBrowse 2: easier track customizaQon
track Qtle tool bar
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GBrowse 2: easier track customizaQon
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GBrowse 2: easier track customizaQon
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GBrowse 2: easier track customizaQon
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GBrowse 2: easier track customizaQon
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click-‐and-‐drag selecQon
GBrowse 2: click-‐and-‐drag zoom
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GBrowse 2: click-‐and-‐drag zoom
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click on ruler
GBrowse 2: ruler
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drag ruler
GBrowse 2: ruler
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GBrowse 2: ruler
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New RNA-‐Seq display opQons: sample selecQon
track configuraRon icon (wrench)
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New RNA-‐Seq display opQons: sample selecQon
verRcal spacing between samples
log2 or linear data display
sample selecRon
Rlted or verRcal data register
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New RNA-‐Seq display opQons: sample selecQon
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New RNA-‐Seq display opQons: linear vs. log2
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ç ç
New RNA-‐Seq display opQons: linear vs. log2
ç
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New RNA-‐Seq display opQons: linear vs. log2
log2 scale linear scale log2 scale linear scale
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í Sequence download: decorated FASTA
í í í
step 1 – choose opRon and hit configure
step 2 – choose opRons
step 3 – hit go
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Sequence download: decorated FASTA
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Other new stuff at FlyBase: NCBI GNOMON annotaQons for Drosophila
GNOMON annotaRons have replaced CAF1 (2006) annotaRons for D. simulans, D. pseudoobscura, D. erecta, D. anannassae and D. yakuba (more on the way). h>p://www.ncbi.nlm.nih.gov/genome/annotaQon_euk/process/
RNA-‐Seq alignment
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Other new stuff at FlyBase: a new D. simulans genome assembly
For more informaRon: h>p://flybase.org/staQc_pages/feature/previous/arQcles/2015_02/Dsim_r2.01.html
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Find this presentaQon on FlyBase
h>p://flybase.org/wiki/FlyBase:FlyBase_Guides:_Pamphlets_and_Powerpoints
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References Brown, et al. (2014). Diversity and dynamics of the Drosophila transcriptome. Nature 512(7515): 393-‐-‐399. (PMID: 24670639, FBrf0225793) dos Santos, et al. (2015). FlyBase: introducRon of the Drosophila melanogaster Release 6 reference genome assembly and large-‐scale migraRon of genome annotaRons. Nucleic Acids Res. 43(Database issue): D690-‐-‐D697. (PMID: 25398896, FBrf0227324) Hoskins, et al. (2015). The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015 Jan 14. pii: gr.185579.114. [Epub ahead of print] (PMID: 25589440) Stein (2013). Using GBrowse 2.0 to visualize and share next-‐generaRon sequence data. Brief Bioinform. 14(2):162-‐-‐171. (PMID: 23376193)