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Integrated Genome Browser Help Desk
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Integrated Genome Browser Help Desk
1–28 of 28
Use this forum to ask questions about
Integrated Genome Browser
.
Useful links about IGB:
Download IGB from
https://bioviz.org
Search the User's Guide at
https://wiki.bioviz.org/
confluence/display/igbman
See which species and genome versions IGB can show at
https://bioviz.org/genome-dash
board
For questions about developing IGB Apps, please visit the
IGB App Developers Forum
.
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David N Levy
,
Nowlan Freese
2
Mar 23
Crashes with trying to save session
Which version of IGB are you using? I will see if I can reproduce the issue on my Mac. To get the IGB
unread,
Crashes with trying to save session
Which version of IGB are you using? I will see if I can reproduce the issue on my Mac. To get the IGB
Mar 23
Nowlan Freese
11/7/22
IGB 9.1.10 released
We are excited to announce that we have released IGB 9.1.10. Some highlights: Fixed an issue where
unread,
IGB 9.1.10 released
We are excited to announce that we have released IGB 9.1.10. Some highlights: Fixed an issue where
11/7/22
Nowlan Freese
7/14/22
Issue with IGB freezing on Mac OS Monterey version 12.3.1 and later
Several users have experienced issues with IGB freezing on Mac OS Monterey version 12.3.1 and later.
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Issue with IGB freezing on Mac OS Monterey version 12.3.1 and later
Several users have experienced issues with IGB freezing on Mac OS Monterey version 12.3.1 and later.
7/14/22
Lingrui Zhang
, …
Nowlan Freese
4
7/14/22
IGB crashes!!!
Hi Rebecca, Please try downloading and installing IGB from this link: https://bitbucket.org/
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IGB crashes!!!
Hi Rebecca, Please try downloading and installing IGB from this link: https://bitbucket.org/
7/14/22
Mason Lee
,
Nowlan Freese
2
7/7/22
Strange Scores on Reads in a Predicted Intron Site
Hi Mason, It looks like the Label Field is set to "scores" in IGB. Assuming that is the
unread,
Strange Scores on Reads in a Predicted Intron Site
Hi Mason, It looks like the Label Field is set to "scores" in IGB. Assuming that is the
7/7/22
Xiao Lei
,
Nowlan Freese
2
4/7/22
IGB depth graph for customer genomes
Hi Xiao, You can create a depth graph from a bam file using IGB Track Operations. To create a depth
unread,
IGB depth graph for customer genomes
Hi Xiao, You can create a depth graph from a bam file using IGB Track Operations. To create a depth
4/7/22
Xiao Lei
,
Ann Loraine
2
4/7/22
IGB version
Hi, Thanks for your question! There are currently two available versions of IGB available from the
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IGB version
Hi, Thanks for your question! There are currently two available versions of IGB available from the
4/7/22
Nowlan Freese
1/25/22
IGB User's Guide new location: wiki.bioviz.org
We have recently finished migrating the IGB User's Guide to a new location: wiki.bioviz.org
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IGB User's Guide new location: wiki.bioviz.org
We have recently finished migrating the IGB User's Guide to a new location: wiki.bioviz.org
1/25/22
Steven Walsh
, …
Nowlan Freese
4
1/25/22
Track Hubs
We are currently developing a site that will allow for the public UCSC track hubs to be visible in
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Track Hubs
We are currently developing a site that will allow for the public UCSC track hubs to be visible in
1/25/22
Xiao Lei
,
Nowlan Freese
2
12/17/21
IGB browser (Mac version 9.1.10) frozen frequently
Hi Xiao, I will see if I can replicate this issue on my Mac. Since you are on the early access
unread,
IGB browser (Mac version 9.1.10) frozen frequently
Hi Xiao, I will see if I can replicate this issue on my Mac. Since you are on the early access
12/17/21
Xiao Lei
,
Nowlan Freese
2
12/17/21
IGB depth graph: solid box vs open box
Hi Xiao, Depending on the level of zoom or data density the graphs may render slightly differently. I
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IGB depth graph: solid box vs open box
Hi Xiao, Depending on the level of zoom or data density the graphs may render slightly differently. I
12/17/21
Xiao Lei
,
Nowlan Freese
2
12/17/21
bug report: certain gene name search result not expected
Hi Xiao, We are aware of this bug. It occurs when using the range and search box if there are
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bug report: certain gene name search result not expected
Hi Xiao, We are aware of this bug. It occurs when using the range and search box if there are
12/17/21
Xiao Lei
,
Ann Loraine
2
11/4/21
overlapped label of genes in IGB
Hi, The reason the labels are shown as overlapping is because the gene model track is currently in
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overlapped label of genes in IGB
Hi, The reason the labels are shown as overlapping is because the gene model track is currently in
11/4/21
Nowlan Freese
9/30/21
Information on Genome Browser coordinates
Here is a link from UCSC that describes the differences between 0-based and 1-based genome
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Information on Genome Browser coordinates
Here is a link from UCSC that describes the differences between 0-based and 1-based genome
9/30/21
Robersy Sanchez
,
Nowlan Freese
3
9/29/21
IGB match wrong coordinate on GRCh37
I double-checked the file on IGB and UCSC, the locations specified in the wig files are correct
unread,
IGB match wrong coordinate on GRCh37
I double-checked the file on IGB and UCSC, the locations specified in the wig files are correct
9/29/21
Nowlan Freese
6/22/21
Are you no longer seeing a particular genome in IGB 9.1.8?
In IGB 9.1.8 the UCSC DAS Data Source is disabled by default. Genomes and data sets provided by UCSC
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Are you no longer seeing a particular genome in IGB 9.1.8?
In IGB 9.1.8 the UCSC DAS Data Source is disabled by default. Genomes and data sets provided by UCSC
6/22/21
Nowlan Freese
6/22/21
UCSC DAS Data Source disabled by default in IGB 9.1.8
In IGB 9.1.8 the UCSC DAS Data Source is disabled by default. Genomes and data sets provided by UCSC
unread,
UCSC DAS Data Source disabled by default in IGB 9.1.8
In IGB 9.1.8 the UCSC DAS Data Source is disabled by default. Genomes and data sets provided by UCSC
6/22/21
Arnaud Ceol
,
Ann Loraine
2
5/17/21
Import tracks from network shares
If the network files systems appear to native applications like ordinary files saved on the local
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Import tracks from network shares
If the network files systems appear to native applications like ordinary files saved on the local
5/17/21
Jason Kuehner
,
Nowlan Freese
2
2/3/21
Changing font size of track labels?
Hi Jason, I don't think we made any recent changes to limit the track Label Font size. If you
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Changing font size of track labels?
Hi Jason, I don't think we made any recent changes to limit the track Label Font size. If you
2/3/21
Dan
,
Nowlan Freese
2
10/28/20
Adding reference genome to IGB
To visualize a custom genome in IGB: Select File > Open Genome from File... (or click the DNA icon
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Adding reference genome to IGB
To visualize a custom genome in IGB: Select File > Open Genome from File... (or click the DNA icon
10/28/20
IGB Helper
,
Chester Dias
2
7/14/20
Q&A
Can't build IGB on Debian (Originally posted to IGB Jira)
Cause of Error: igb-javafx-util: Compilation failure This package needs java fx to be present.
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Q&A
Can't build IGB on Debian (Originally posted to IGB Jira)
Cause of Error: igb-javafx-util: Compilation failure This package needs java fx to be present.
7/14/20
benjami...@brown.edu
,
nowlan...@gmail.com
2
6/29/20
Custom Quickload Troubleshooting
Hi Ben, Glad we were able to figure out the issue today. Let me know if you run into anything else
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Custom Quickload Troubleshooting
Hi Ben, Glad we were able to figure out the issue today. Let me know if you run into anything else
6/29/20
Benjamin Styler
, …
Ann Loraine
3
6/26/20
Q&A
Uploading to IGB Quickload?
Thank you again for the question - thank for your patience! The instructions are correct, and if you
unread,
Q&A
Uploading to IGB Quickload?
Thank you again for the question - thank for your patience! The instructions are correct, and if you
6/26/20
IGB Helper
6/15/20
Q&A
Problem with Schizosaccharomyces pombe genome (Orginally posted to IGB Jira)
An IGB user reported: Hello, I just wanted to report a bug concerning Schizosaccharomyces pombe
unread,
Q&A
Problem with Schizosaccharomyces pombe genome (Orginally posted to IGB Jira)
An IGB user reported: Hello, I just wanted to report a bug concerning Schizosaccharomyces pombe
6/15/20
IGB Helper
6/15/20
Q&A
How to get IGB to use color specified in GFF
A couple of IGB users asked us about configuring color settings using track lines in GFF format files
unread,
Q&A
How to get IGB to use color specified in GFF
A couple of IGB users asked us about configuring color settings using track lines in GFF format files
6/15/20
IGB Helper
6/8/20
Q&A
Genome not available at this time (Originally posted to IGB Jira)
In Jan 2020, an IGB user posted the following question to the IGB Jira board: When I open IGB it
unread,
Q&A
Genome not available at this time (Originally posted to IGB Jira)
In Jan 2020, an IGB user posted the following question to the IGB Jira board: When I open IGB it
6/8/20
IGB Helper
6/8/20
Q&A
Can't load multi-track BED file into IGB (originally posted on BioStars)
An IGB user posted the following question on the BioStars Web site: I have BED files of some ChIP-seq
unread,
Q&A
Can't load multi-track BED file into IGB (originally posted on BioStars)
An IGB user posted the following question on the BioStars Web site: I have BED files of some ChIP-seq
6/8/20
IGB Helper
5/21/20
Q&A
How do I load data into IGB?
Loading data in IGB is a three-step process. Step 1: To start, open the genome version for your data
unread,
all-questions
Q&A
How do I load data into IGB?
Loading data in IGB is a three-step process. Step 1: To start, open the genome version for your data
5/21/20