search

igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
646 stars 387 forks source link

Inquiry About Overlaying .bed and .narrowPeak Files in IGV #1506

Open tianliu9 opened 8 months ago

tianliu9 commented 8 months ago

Dear IGV Support Team,

I hope this message finds you well. I would like to ask is it possible to overlay two .bed files or two .narrowPeak files in IGV? I've tried and was only able to overlay two .bigwig files.

Best, Tian

jrobinso commented 8 months ago

No you cannot overlay bed or narrowPeak files, only "wig" type files.

maximilianh commented 8 months ago

I don't understand what the application of this could be.

On the UCSC browser, we now allow drawing features on top of features, which may be related: https://genome.ucsc.edu/goldenPath/help/decorator.html but I'm not sure what the original use case is.

On Wed, Mar 20, 2024 at 1:15 AM Jim Robinson @.***> wrote:

No you cannot overlay bed or narrowPeak files, only "wig" type files.

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2008383823, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TOXHBYYWTHMC25YXXTYZDIJBAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBYGM4DGOBSGM . You are receiving this because you are subscribed to this thread.Message ID: @.***>

tianliu9 commented 7 months ago

Hi Maximilian,

I hope you're doing well. The reason why I asked about this is because one of our PIs would like to overlay .narrowPeak files to identify potential differential peaks across our samples. I wanted to get your take on this approach—do you think this is reasonable? Or I need to proceed directly with a differential expression analysis instead.

Thank you for your time and looking forward to your response.

Thanks, Tian

On Wed, Mar 20, 2024 at 6:27 AM Maximilian Haeussler < @.***> wrote:

I don't understand what the application of this could be.

On the UCSC browser, we now allow drawing features on top of features, which may be related: https://genome.ucsc.edu/goldenPath/help/decorator.html but I'm not sure what the original use case is.

On Wed, Mar 20, 2024 at 1:15 AM Jim Robinson @.***> wrote:

No you cannot overlay bed or narrowPeak files, only "wig" type files.

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2008383823, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AACL4TOXHBYYWTHMC25YXXTYZDIJBAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBYGM4DGOBSGM>

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2009222323, or unsubscribe https://github.com/notifications/unsubscribe-auth/AYXXLQ2O7WJTURNE5QUIZJ3YZFQAVAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBZGIZDEMZSGM . You are receiving this because you authored the thread.Message ID: @.***>

maximilianh commented 7 months ago

Hi, I don't know what you mean with "overlay narrowPeak" files. I don't think any genome browser can overlay individual features, there usually is no need, you can just plot them at the same time and that should look OK. Have you tried that ? Otherwise, maybe you can provide more details what you mean with "overlay" here...

On Mon, Apr 8, 2024 at 7:25 AM tianliu9 @.***> wrote:

Hi Maximilian,

I hope you're doing well. The reason why I asked about this is because one of our PIs would like to overlay .narrowPeak files to identify potential differential peaks across our samples. I wanted to get your take on this approach—do you think this is reasonable? Or I need to proceed directly with a differential expression analysis instead.

Thank you for your time and looking forward to your response.

Thanks, Tian

On Wed, Mar 20, 2024 at 6:27 AM Maximilian Haeussler < @.***> wrote:

I don't understand what the application of this could be.

On the UCSC browser, we now allow drawing features on top of features, which may be related: https://genome.ucsc.edu/goldenPath/help/decorator.html but I'm not sure what the original use case is.

On Wed, Mar 20, 2024 at 1:15 AM Jim Robinson @.***> wrote:

No you cannot overlay bed or narrowPeak files, only "wig" type files.

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2008383823, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AACL4TOXHBYYWTHMC25YXXTYZDIJBAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBYGM4DGOBSGM>

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2009222323, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AYXXLQ2O7WJTURNE5QUIZJ3YZFQAVAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBZGIZDEMZSGM>

. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2041889038, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TKUJXEIB7ZPCICZN4LY4IS3DAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRHA4DSMBTHA . You are receiving this because you commented.Message ID: @.***>

tianliu9 commented 7 months ago

Thank you for getting back to me! Yes, I've already taken that step. At this moment, I don't have any further questions. Many thanks.

Tian

On Mon, Apr 8, 2024 at 9:19 AM Maximilian Haeussler < @.***> wrote:

Hi, I don't know what you mean with "overlay narrowPeak" files. I don't think any genome browser can overlay individual features, there usually is no need, you can just plot them at the same time and that should look OK. Have you tried that ? Otherwise, maybe you can provide more details what you mean with "overlay" here...

On Mon, Apr 8, 2024 at 7:25 AM tianliu9 @.***> wrote:

Hi Maximilian,

I hope you're doing well. The reason why I asked about this is because one of our PIs would like to overlay .narrowPeak files to identify potential differential peaks across our samples. I wanted to get your take on this approach—do you think this is reasonable? Or I need to proceed directly with a differential expression analysis instead.

Thank you for your time and looking forward to your response.

Thanks, Tian

On Wed, Mar 20, 2024 at 6:27 AM Maximilian Haeussler < @.***> wrote:

I don't understand what the application of this could be.

On the UCSC browser, we now allow drawing features on top of features, which may be related: https://genome.ucsc.edu/goldenPath/help/decorator.html but I'm not sure what the original use case is.

On Wed, Mar 20, 2024 at 1:15 AM Jim Robinson @.***> wrote:

No you cannot overlay bed or narrowPeak files, only "wig" type files.

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2008383823,

or

unsubscribe <

https://github.com/notifications/unsubscribe-auth/AACL4TOXHBYYWTHMC25YXXTYZDIJBAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBYGM4DGOBSGM>

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2009222323, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AYXXLQ2O7WJTURNE5QUIZJ3YZFQAVAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBZGIZDEMZSGM>

. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2041889038, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AACL4TKUJXEIB7ZPCICZN4LY4IS3DAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRHA4DSMBTHA>

. You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2042741980, or unsubscribe https://github.com/notifications/unsubscribe-auth/AYXXLQ6QHLUV3LJ55N5F67LY4KKPRAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBSG42DCOJYGA . You are receiving this because you authored the thread.Message ID: @.***>

maximilianh commented 7 months ago

BED decorators allow you to overlay peaks transparently, https://genome.ucsc.edu/goldenPath/help/decorator.html, as I had mentioned above, but I don't know if that would solve your problem as I haven't fully understood what this PI expects to see...

On Tue, Apr 9, 2024 at 10:12 PM tianliu9 @.***> wrote:

Thank you for getting back to me! Yes, I've already taken that step. At this moment, I don't have any further questions. Many thanks.

Tian

On Mon, Apr 8, 2024 at 9:19 AM Maximilian Haeussler < @.***> wrote:

Hi, I don't know what you mean with "overlay narrowPeak" files. I don't think any genome browser can overlay individual features, there usually is no need, you can just plot them at the same time and that should look OK. Have you tried that ? Otherwise, maybe you can provide more details what you mean with "overlay" here...

On Mon, Apr 8, 2024 at 7:25 AM tianliu9 @.***> wrote:

Hi Maximilian,

I hope you're doing well. The reason why I asked about this is because one of our PIs would like to overlay .narrowPeak files to identify potential differential peaks across our samples. I wanted to get your take on this approach—do you think this is reasonable? Or I need to proceed directly with a differential expression analysis instead.

Thank you for your time and looking forward to your response.

Thanks, Tian

On Wed, Mar 20, 2024 at 6:27 AM Maximilian Haeussler < @.***> wrote:

I don't understand what the application of this could be.

On the UCSC browser, we now allow drawing features on top of features, which may be related: https://genome.ucsc.edu/goldenPath/help/decorator.html but I'm not sure what the original use case is.

On Wed, Mar 20, 2024 at 1:15 AM Jim Robinson @.***> wrote:

No you cannot overlay bed or narrowPeak files, only "wig" type files.

— Reply to this email directly, view it on GitHub < https://github.com/igvteam/igv/issues/1506#issuecomment-2008383823>,

or

unsubscribe <

https://github.com/notifications/unsubscribe-auth/AACL4TOXHBYYWTHMC25YXXTYZDIJBAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBYGM4DGOBSGM>

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2009222323,

or

unsubscribe <

https://github.com/notifications/unsubscribe-auth/AYXXLQ2O7WJTURNE5QUIZJ3YZFQAVAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBZGIZDEMZSGM>

. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2041889038, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AACL4TKUJXEIB7ZPCICZN4LY4IS3DAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRHA4DSMBTHA>

. You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2042741980, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AYXXLQ6QHLUV3LJ55N5F67LY4KKPRAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBSG42DCOJYGA>

. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2046550497, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TOD2YIY5VZUHXA4JIDY4TC3RAVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBWGU2TANBZG4 . You are receiving this because you commented.Message ID: @.***>

jrobinso commented 7 months ago

Also, to clarify BED decorators are an option for the UCSC Genome Browser, IGV does not have this feature.

maximilianh commented 7 months ago

Oops, sorry, and thanks Jim, I totally forgot that this is the IGV ticketing system... too many tickets in my inbox...

On Wed, Apr 10, 2024 at 12:04 PM Jim Robinson @.***> wrote:

Also, to clarify BED decorators are an option for the UCSC Genome Browser, IGV does not have this feature.

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv/issues/1506#issuecomment-2048249376, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TJGVHDQSH7RX6EDL6LY4WEK5AVCNFSM6AAAAABE6NOIUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBYGI2DSMZXGY . You are receiving this because you commented.Message ID: @.***>