igv-help

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Welcome to the help and discussion forum for the Integrative Genomics Viewer (IGV). If posting about a problem, please include:

The version of IGV you are using, and your computer operating system.
What you did. If the problem happens when you open a file and/or view certain genomic coordinates, attach the file* (or provide a link) and specify the genomic coordinates. Please DO NOT paste the contents of your file into an email or in the group's web interface, as files are whitespace sensitive which gets lost when sent in the body of an email.
Your igv0.log file. It will be in <your home directory>/igv.

About this forum: Anyone can browse the messages previously posted in this forum. To post new questions, bug reports, and suggestions, please join the group. If you don't have a Google account, sign up by sending an email to igv-help+subscribe@googlegroups.com with "subscribe" as the subject.

Alternatively, you can create issues in our code repositories at https://github.com/igvteam. Note we have separate repositories for the IGV desktop application, the igv.js JavaScript component, and the IGV-Web app.

For more info about IGV, see https://igv.org.

0 selected

Eliana Garzon, igv-help2

11:48 AM

Remove duplicate reads

If the reads are flagged as duplicate in the BAM file you can filter them out from the IGV view by

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Remove duplicate reads

If the reads are flagged as duplicate in the BAM file you can filter them out from the IGV view by

11:48 AM

Achim Schnaufer, … James Robinson7

Apr 24

Cannot launch IGV under Windows 10

I think we have a semantics issue here, the release you refer to is a maintenance (bug fix) release

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Cannot launch IGV under Windows 10

I think we have a semantics issue here, the release you refer to is a maintenance (bug fix) release

Apr 24

hou ri, igv-help6

Apr 22

Interpreting Color by Pair Orientation

We find your comments to be highly valuable. Additionally, we believe there are issues with the

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Interpreting Color by Pair Orientation

We find your comments to be highly valuable. Additionally, we believe there are issues with the

Apr 22

Poorvi Dua, igv-help2

Apr 22

5' Untranslated Region Annotations

If you mouse over the gene track it will show you the URL of the source file. The Refseq Genes track

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5' Untranslated Region Annotations

If you mouse over the gene track it will show you the URL of the source file. The Refseq Genes track

Apr 22

Gennady Margolin, igv-help4

Apr 19

ENSEMBL chromosome names (e.g., 1 instead of chr1) don't work in desktop app

Hi, that fixed it - thanks so much! On Friday, April 19, 2024 at 2:48:53 AM UTC-4 igv-help wrote: Hi,

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ENSEMBL chromosome names (e.g., 1 instead of chr1) don't work in desktop app

Hi, that fixed it - thanks so much! On Friday, April 19, 2024 at 2:48:53 AM UTC-4 igv-help wrote: Hi,

Apr 19

Adam Clayton, igv-help7

Apr 18

Similar bed files not showing data in whole genome view

Yes, I've confirming things are working in the latest snapshot build. Thanks for following up. -

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Similar bed files not showing data in whole genome view

Yes, I've confirming things are working in the latest snapshot build. Thanks for following up. -

Apr 18

Peter Doris, … James Robinson8

Apr 17

2.17.0 wont' work, there is a specific GenArk menu in 2.17.4. On Wed, Apr 17, 2024 at 12:25 PM

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2.17.0 wont' work, there is a specific GenArk menu in 2.17.4. On Wed, Apr 17, 2024 at 12:25 PM

Apr 17

Peter O'Reilly, igv-help3

Apr 17

Getting a larger consensus sequence from alignments

Thank you for the response! I will look at the user guide more thoroughly. We have a new lab computer

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Getting a larger consensus sequence from alignments

Thank you for the response! I will look at the user guide more thoroughly. We have a new lab computer

Apr 17

Nancy De Nève, igv-help2

Apr 16

Question about white strands

The hollow/white alignments have a mapping quality (MAPQ) value of zero in the BAM file. The exact

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Question about white strands

The hollow/white alignments have a mapping quality (MAPQ) value of zero in the BAM file. The exact

Apr 16

Kartik Singhal, igv-help2

Apr 16

IGV Web App GC% track

Hi Kartik, Thanks for letting us know. The IGV-Web menu retrieves data from servers at UCSC, and

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IGV Web App GC% track

Hi Kartik, Thanks for letting us know. The IGV-Web menu retrieves data from servers at UCSC, and

Apr 16

Yulia Kentieva, … James Robinson4

Apr 15

Loading genome file takes 8+ hrs

It looks loaded to me. Do you mean a gene annotation track? The fasta just defines the reference

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Loading genome file takes 8+ hrs

It looks loaded to me. Do you mean a gene annotation track? The fasta just defines the reference

Apr 15

Jennifer Huellein, igv-help3

Apr 12

Loading custom gene annotation fails (Cannot determine file type)

Note if you get a page not found error when you click on the above link, paste the text into your

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Loading custom gene annotation fails (Cannot determine file type)

Note if you get a page not found error when you click on the above link, paste the text into your

Apr 12

Limin Chen, igv-help3

Apr 11

IGV_2.16.2 in Windows 11 shows completely different appearance from Mac

Hi Helga, Thank you so much for the help. It works now following your advice. Just to update in IGV_2

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IGV_2.16.2 in Windows 11 shows completely different appearance from Mac

Hi Helga, Thank you so much for the help. It works now following your advice. Just to update in IGV_2

Apr 11

Simon Andrews, igv-help4

Apr 9

Can't load BAM file into web version of IGV

Hi, yes thanks for letting us know. Just some clarification for those that might find this thread.

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Can't load BAM file into web version of IGV

Hi, yes thanks for letting us know. Just some clarification for those that might find this thread.

Apr 9

Katie Aney, igv-help2

Apr 8

Issue viewing bam on browser (but not desktop app)

Hi Kate, First, when you are loading the file into IGV-Web, where are you loading it from? Is it via

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Issue viewing bam on browser (but not desktop app)

Hi Kate, First, when you are loading the file into IGV-Web, where are you loading it from? Is it via

Apr 8

Tori Earl, igv-help3

Apr 3

Naming convention causing issues in new version

Hi, thanks for the test data. This is a bug that will potentially affect any genome assembly with a

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Naming convention causing issues in new version

Hi, thanks for the test data. This is a bug that will potentially affect any genome assembly with a

Apr 3

Brew Belly, … James Robinson5

Apr 3

Error Loading Wig Tracks

Your screenshot indicates a fasta sequence name of "BW30270i", however the wig variable

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Error Loading Wig Tracks

Your screenshot indicates a fasta sequence name of "BW30270i", however the wig variable

Apr 3

Bradley Balk, igv-help2

Mar 31

Problem loading in Encode data.

That indicates a network timeout, but we need more information. Exactly what Encode data, and what

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Problem loading in Encode data.

That indicates a network timeout, but we need more information. Exactly what Encode data, and what

Mar 31

Thaysa Lopes, … John Lattier3

Mar 27

Links opening on browser

Seen the same issues for years. Old version IGV + Old version Excel = works fine New version IGV +

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Links opening on browser

Seen the same issues for years. Old version IGV + Old version Excel = works fine New version IGV +

Mar 27

Petra Platen, igv-help4

Mar 23

new Reference Genome

Hi, Helga is on vacation. The easiest way to load this is to use the menu item she described from IGV

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new Reference Genome

Hi, Helga is on vacation. The easiest way to load this is to use the menu item she described from IGV

Mar 23

Alba Muñoz Santa, igv-help2

Mar 23

Doubt about the Error Message; "Does not contain any sequence names which match the current genome."

The sequence names do not match, your BAM file has the sequence name "NC_002516.2", the

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Doubt about the Error Message; "Does not contain any sequence names which match the current genome."

The sequence names do not match, your BAM file has the sequence name "NC_002516.2", the

Mar 23

Dario Dilernia, igv-help2

Mar 23

Color by base modification not displaying

The base mod options are in the right-click menu, right-click over the alignment track and you will

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Color by base modification not displaying

The base mod options are in the right-click menu, right-click over the alignment track and you will

Mar 23

Rachel Melamed, igv-help2

Mar 22

obtaining BAM files from "load from Encode 2012"

Hi, BAM files from Encode have never been available through the IGV menu. This is not possible

unread,

obtaining BAM files from "load from Encode 2012"

Hi, BAM files from Encode have never been available through the IGV menu. This is not possible

Mar 22

Sarin Aryal, … igv-help4

Mar 21

Group autoscale of multiple tracks

Its not released yet, but will be soon. It is checked in to the master branch. Also you can try it

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Group autoscale of multiple tracks

Its not released yet, but will be soon. It is checked in to the master branch. Also you can try it

Mar 21

ruisi wang, … James Robinson5

Mar 21

operation not permitted

Got it! Will try! Thank you so much! On Mar 20, 2024, at 10:28 PM, 'James Robinson' via igv-

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operation not permitted

Got it! Will try! Thank you so much! On Mar 20, 2024, at 10:28 PM, 'James Robinson' via igv-

Mar 21

Mar 20

Bed graph plot tools

Dear, I want to create a similar plot. Can anyone point me to the tool/s for creating such plot.

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Bed graph plot tools

Dear, I want to create a similar plot. Can anyone point me to the tool/s for creating such plot.

Mar 20

Daniel Jeronimo, igv-help5

Mar 19

That would be a question for the data source, IGV is just displaying what are in the files. On

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That would be a question for the data source, IGV is just displaying what are in the files. On

Mar 19

Thomas, … James Robinson7

Mar 19

igv does not always display sashimi plots

Hi. I understand now. I deleted the IGV-generated genome folder that carried the genome information

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igv does not always display sashimi plots

Hi. I understand now. I deleted the IGV-generated genome folder that carried the genome information

Mar 19

Ian Brabb, igv-help5

Mar 15

Large RNAseq bedgraphs (zipped) too large to load

Never mind my earlier questions, it doesn't matter. The problematic bedgraph files are more the

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Large RNAseq bedgraphs (zipped) too large to load

Never mind my earlier questions, it doesn't matter. The problematic bedgraph files are more the

Mar 15

Jesse Huerta, igv-help9

Mar 15

Error installing IGV

Glad to hear it. On Friday, March 15, 2024 at 5:19:16 PM UTC-4 jessej...@tamu.edu wrote: Thank you, I

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Error installing IGV

Glad to hear it. On Friday, March 15, 2024 at 5:19:16 PM UTC-4 jessej...@tamu.edu wrote: Thank you, I

Mar 15

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