Integrated Genome Browser Help Desk

Contact owners and managers

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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-dashboard

For questions about developing IGB Apps, please visit the IGB App Developers Forum.

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Nowlan Freese, 加藤紗智4

12:30 AM

IGB 10.0.0 released

Hi Nowlan, Thank you for your advice and let me know about IGB version. I will try it! Sachi 2024年4月

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IGB 10.0.0 released

Hi Nowlan, Thank you for your advice and let me know about IGB version. I will try it! Sachi 2024年4月

12:30 AM

Nowlan Freese

Mar 28

Known issue where spaces in file or folder names can cause files not to load in IGB

We are aware and are working on an issue where bigwig and bigbed files fail to load in IGB 10.0.0.

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Known issue where spaces in file or folder names can cause files not to load in IGB

We are aware and are working on an issue where bigwig and bigbed files fail to load in IGB 10.0.0.

Mar 28

Nowlan Freese2

Mar 26

macOS 14.4 update on Apple silicon (M1, M2, M3) will cause Java programs such as IGB to crash

The macOS 14.4.1 update should fix the issue with Java programs crashing. Please let us know if you

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macOS 14.4 update on Apple silicon (M1, M2, M3) will cause Java programs such as IGB to crash

The macOS 14.4.1 update should fix the issue with Java programs crashing. Please let us know if you

Mar 26

IGB Helper

Mar 4

Weekly Office Hours

Starting this week, we will be holding weekly office hours to answer any questions you might have

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Weekly Office Hours

Starting this week, we will be holding weekly office hours to answer any questions you might have

Mar 4

Nowlan Freese, Nowlan Freese2

Feb 12

Genome not available at this time. Please check that the appropriate data source is available.

The issue has been resolved. If you added the temporary workaround and are now seeing two gene

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Genome not available at this time. Please check that the appropriate data source is available.

The issue has been resolved. If you added the temporary workaround and are now seeing two gene

Feb 12

Marisa Faustino, … Nowlan Freese10

12/22/23

IGB Mac Ventura 13.5

We are preparing a major update to IGB that appears to fix the issue on our Apple laptops. We will be

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IGB Mac Ventura 13.5

We are preparing a major update to IGB that appears to fix the issue on our Apple laptops. We will be

12/22/23

Lakshmi Mahendrawada, … Nowlan Freese6

12/22/23

IGB app takes very long time to open in Mac

Hi Lakshmi, We are preparing a major update to IGB that may fix this issue. We will be releasing the

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IGB app takes very long time to open in Mac

Hi Lakshmi, We are preparing a major update to IGB that may fix this issue. We will be releasing the

12/22/23

Emilia Dimitrova, Nowlan Freese3

12/21/23

IGB has stopped loading

If you would like to try out our newest build of IGB for Windows, the link is below. Note that this

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IGB has stopped loading

If you would like to try out our newest build of IGB for Windows, the link is below. Note that this

12/21/23

Leena Shah, Nowlan Freese2

6/21/23

Conversion of raw data into bedgraph files

Hi Leena, The supplementary file data at the GEO link (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi

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Conversion of raw data into bedgraph files

Hi Leena, The supplementary file data at the GEO link (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi

6/21/23

Leena Shah, Nowlan Freese2

6/9/23

Converting XLSX files into BED or BAM files

I converted the files to bedgraph since that's what the data resembled to me. Let me know if this

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Converting XLSX files into BED or BAM files

I converted the files to bedgraph since that's what the data resembled to me. Let me know if this

6/9/23

Jonathan Monin, … Stay with Rezanur & Tania4

5/6/23

mm39

Dear Nowlan Thank you so much. I also had this issue and now resolved. I'll post some queries if

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mm39

Dear Nowlan Thank you so much. I also had this issue and now resolved. I'll post some queries if

5/6/23

David N Levy, Nowlan Freese2

3/23/23

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

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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

3/23/23

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

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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 Freese4

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 Freese2

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

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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 Freese2

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

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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 Loraine2

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 Freese4

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 Freese2

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

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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 Freese2

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 Freese2

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 Loraine2

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 Freese3

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

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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

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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 Loraine2

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 Freese2

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