Comments (5)
from ularcirc.
Hi
Thanks for replying.
Renaming the file solved the uploading problem. I have another issue.
I'm using the C. elegans genome. I loaded the genome and refGene data.
Then I upload the Circexplorer2 output file using "sample.ce" as its name without any problem.
However, when I navigated to Gene_view panel, a warning message appeared.
Loading species transcriptome coordinates Thu Sep 12 14:37:29 2019
Displaying list of 46857 genes built Thu Sep 12 14:37:29 2019
Loading data s1.ce
Loading data 229190
Loading data
Loading data C:\Users\DC\AppData\Local\Temp\RtmpSC9dj8/f3015252fea6a6872340408c/0.ceWarning in IdentifyDataSets() :
No data loaded or selected so nothing to display
Please navigate back to PROJECT tab and load a data set
I can build the BSJ table as below:
But when I chose one gene to show the transcript, another error appeared.
Requesting Gene Object for zip-2 Thu Sep 12 14:46:26 2019Warning: Error in if: argument is of length zero
185: [C:\Program Files\R\R-3.6.1\library\Ularcirc\shiny-app\circRNA/server.R#2604]
183: .func
180: contextFunc
179: env$runWith
172: ctx$run
171: self$.updateValue
169: circRNA_Subset
168: renderPlot [C:\Program Files\R\R-3.6.1\library\Ularcirc\shiny-app\circRNA/server.R#3731]
166: func
126: drawPlot
112: reactive:plotObj
96: drawReactive
83: origRenderFunc
82: output$plotFSJ_BSJ_GeneModel
2: shiny::runApp
1: Ularcirc
Warning: Error in if: argument is of length zero
100:
Can you help with this?
Thank you.
from ularcirc.
I suspect this might be a coding error relating to no FSJ file being present. As you aligned data with STAR would you mind uploading the SJ.tab.out file. To do this rename the SJ.tab.out to have the same file prefix (which in your case would be s1.SJ.out.tab).
Note you will have to upload both s1.SJ.out.tab and s1.ce at the same time. Therefore make sure both files are in the same directory/folder so that you can select them both.
Let me know if this fixes the situation as this will confirm that I need to put another checkpoint in code.
from ularcirc.
Hi David
Yes, it works after uploading the SJ.tab.out and Circexplorer2 file.
Thank you for your great help.
from ularcirc.
Have updated code which should catch filename errors.
from ularcirc.
Related Issues (20)
- Large File Silently Added To User Home Directory HOT 2
- Genomic Information Not Retrieved for Any Junction HOT 8
- installation error (Failed to install 'Ularcirc' from GitHub) HOT 1
- PDF Export Default Extension is CSV
- Result Table Column Explanations HOT 1
- installation
- Problem with BS junction sequences HOT 3
- Ularcirc crashing with STAR data and gene annotation HOT 3
- BS junction sequences: one-base shift HOT 2
- How to bring in custom annotations (BSgenome, TxDb)? HOT 4
- Couldn't visit Youtube HOT 2
- Bug reports when using Ensembl ID based de novo assembly transcriptome for the species other than human HOT 2
- Step 2 Not Working HOT 1
- Essential Dependencies Not Installed Automatically HOT 1
- Annotate With Parental Gene Missing HOT 2
- Name Prefix Must End with Period But Not Documented HOT 1
- Chimeric File Crashes Ularcirc HOT 3
- Gene Count Table Requirements Missing HOT 2
- loadSTAR_chimeric Missing HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ularcirc.