WashU Epigenome Browser

02/19/2014

11:19 am Bug #165 (Closed): browser frozen when panning of BAM tracks

* Thanks for fixing! Daofeng Li

11:07 am Bug #165 (Resolved): browser frozen when panning of BAM tracks

Fixed in v32.1.8! Xin Zhou

10:15 am Bug #165 (Closed): browser frozen when panning of BAM tracks

* using this hub: http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://cgs.wustl.edu/~dli/C... Daofeng Li

10:13 am Bug #164 (Closed): UI frozen when click 'remove all' from json hub

Daofeng Li

10:11 am Bug #164 (Resolved): UI frozen when click 'remove all' from json hub

Fixed in v32.1.7. Thanks! Xin Zhou

09:58 am Bug #164 (Closed): UI frozen when click 'remove all' from json hub

* loading this hub: http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://cgs.wustl.edu/~dli... Daofeng Li

02/18/2014

03:39 pm Bug #163 (New): long responsive time while track missed in hub

* see Junchen's hub at http://remc.wustl.edu/jgu/human/remc/methylomes/methylomes_all_hub.json
* apache error log sh... Daofeng Li

08:02 am Feature #162 (Resolved): Tooltip information

Implemented in v32.1.4. Thanks! Xin Zhou

02/15/2014

01:09 pm Bug #160 (Resolved): Custom PE BAM files unstable

Fixed in v32.1.4
http://epigenomegateway.wustl.edu/browser/?genome=danRer7&custombam=xx,http://cgs.wustl.edu/~rlow... Xin Zhou

08:00 am Bug #153: track information display error

Missing GEO accession has been fixed. Xin Zhou

02/14/2014

10:18 pm Bug #147 (Closed): crash when track file not exist in json hub

fixed. Daofeng Li

10:17 pm Bug #153: track information display error

GEO links also could not be recovered? Daofeng Li

04:46 pm Bug #159 (Closed): Session not saving

Xin Zhou

04:45 pm Bug #155: browser url parameter for coordinate not working

Use the "native_track" keyword and add gene track to your JSON datahub.
Find example in this hub:
http://vizhub... Xin Zhou

04:43 pm Bug #155: browser url parameter for coordinate not working

OK. I see.
Then how do I include the gene annotation track by default with my own data? When I uploaded my own tr... Junchen Gu

04:43 pm Bug #157: refSeq gene position didn't keep in session

refSeq is a "native track". Current design only keeps order of custom tracks. Native tracks are all piled to the bottom. Xin Zhou

04:29 pm Bug #155 (Rejected): browser url parameter for coordinate not working

When the "session" and "statusId" parameters are in use, the "coordinate" parameter is disregarded, since the view ra... Xin Zhou

04:25 pm Bug #153 (Resolved): track information display error

Fixed in v32.1.3, but the track details from previous saved sessions cannot be recovered. Xin Zhou

03:58 pm Bug #147 (Resolved): crash when track file not exist in json hub

can you try again with the new code? Xin Zhou

03:31 pm Feature #162 (Closed): Tooltip information

Would be great if the tooltip could include per-read CIGAR strings, mapping quality scores, and maybe insert size inf... Rebecca Lowdon

02/13/2014

05:59 pm Feature #158: wrapping for tooltip read information

good suggestion :) Daofeng Li

05:58 pm Bug #159: Session not saving

my bad, wrong permission for the session folder. Should be fixed now. Please let me know if problem still exists. Daofeng Li

03:32 pm Feature #161 (New): Include scaffolds on genome snapshot

Would be nice to view scaffolds and unassigned chromosome fragments (in danRer7 referred to as "NA###") in the "genom... Rebecca Lowdon

03:27 pm Bug #160 (Closed): Custom PE BAM files unstable

BAM tracks of paired-end alignments appear unstable on the browser. Relocating or zooming in/out causes reads to "mov... Rebecca Lowdon

03:20 pm Bug #159 (Closed): Session not saving

Was trying to save a session to send you another bug ... but sessions not working on danRer7! Rebecca Lowdon

03:18 pm Feature #158 (New): wrapping for tooltip read information

Would be nice if information in tooltip would automatically wrap to display all information. For example, I want to v... Rebecca Lowdon

02/11/2014

10:52 pm Bug #123 (Closed): embedded browser cannot handle hidden tracks

Daofeng Li

10:52 pm Feature #145 (Closed): loose format requirement for coordinates format

* yes, it works great! Daofeng Li

10:52 pm Bug #152 (Closed): clicking "zoom in" button makes browser unresponsive

Daofeng Li

10:51 pm Bug #148 (Closed): add geneset to genome snapshot error

Daofeng Li

10:50 pm Bug #157 (New): refSeq gene position didn't keep in session

* move refSeq gene to top of canvas
* same session, load, the refSeq gene goes to bottom Daofeng Li

02/07/2014

11:45 pm washugb v32 release

* We have released v32 of WashU EpiGenome Browser.
h2. Updates
* shared metadata, for details please see: http:... Daofeng Li

11:32 pm Complete Epigenome Browser Bug #156 (New): WUGB popup link get blocked

* the popup being blocked seems are default behavior of most modern browsers
Daofeng Li

04:11 pm Bug #155 (Rejected): browser url parameter for coordinate not working

Xin,
If you go to my Feb. 2014 wiki and on Feb. 6-7, I have a table of regions and in the last column there are brow... Junchen Gu

02/06/2014

02:11 pm Bug #154 (Resolved): Cannot search for gene in embedded browser

Fixed in v32.0.7.
See this example: http://cgs.wustl.edu/~xzhou/embed/1.html Xin Zhou

02:04 pm Bug #154 (Closed): Cannot search for gene in embedded browser

If the embedded browser only imports "base.js" it can't search and jump to a gene, this error will be given:
Objec... Xin Zhou

02/05/2014

12:31 pm Bug #153 (Closed): track information display error

* same a session, load it with the link generated
* right click a track, choose Information, you will see some infor... Daofeng Li

10:32 am Bug #152 (Resolved): clicking "zoom in" button makes browser unresponsive

Fixed in v32.0.3 on public browser
The bug is still there on test server for you to check out. Xin Zhou

10:31 am Bug #152 (Closed): clicking "zoom in" button makes browser unresponsive

CLick the "+" (zoom in) button multiple times until getting this message:
At finest level, cannot zoom in
And t... Xin Zhou

02/01/2014

08:35 am Feature #145 (Resolved): loose format requirement for coordinates format

Fixed in v32.0.1. Try these coordinates with multiple spaces separating fields:
chr7 55418829 55419003
chr7... Xin Zhou

01/31/2014

08:41 am Bug #119 (Closed): fixedscale and track height probem in json hub

Daofeng Li

08:40 am Bug #144 (Closed): mouse over event for meta data header ( in track table ) disappear

Daofeng Li

08:40 am Bug #150 (Closed): js error and clickable 'None yet'

Daofeng Li

08:31 am Bug #150 (Resolved): js error and clickable 'None yet'

Fixed, thanks for finding out this tricky problem! Xin Zhou

12:19 am Bug #150 (Closed): js error and clickable 'None yet'

* the js errors in the console seems happened when open 2nd panel, while no crash happens
* the 'None yet' in 'custo... Daofeng Li

01/30/2014

06:50 am Bug #149 (Rejected): possible coordinate issue

Xin Zhou

06:50 am Bug #149: possible coordinate issue

Thanks for reporting this. This is because our browser's coordinates are 0-offset, they all start from 0. But in UCSC... Xin Zhou

01:09 am Bug #149 (Rejected): possible coordinate issue

I was looking at a SNP (chr16:89986117-89986117) which is a C shown on UCSC browser (see attached image) but it's a G... Junchen Gu

01/28/2014

07:20 am Bug #148 (Resolved): add geneset to genome snapshot error

Fixed, thanks! Xin Zhou

01/27/2014

05:22 pm Bug #148 (Closed): add geneset to genome snapshot error

* submit a list of coordinates to gene set
* looks like browser didn't give a default name for the list, when you cl... Daofeng Li

03:11 pm Bug #147 (Closed): crash when track file not exist in json hub

* I found if I renamed a file in my hub, loading the hub without updating it, browser will throw 'Json syntax error' Daofeng Li