[Gmod-ajax] Allele column from BAM?

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[Gmod-ajax] Allele column from BAM?

Keiran Raine
Hi,

Does anyone know of a plugin that could produce a fixed height track which gives a fractional ACGT colour based stack for each position?

We generate deep sequence amplicon data and need a way to display the data using less screen real estate, but I see this as generally useful for Alignment tracks.

What I'd ideally be looking for is a track that would stack from most prevelant non-ref base and switch the colour for the ref base to grey.

e.g.

REF = A
Reads:
A=50 - position 4
C=30 - position 1
G=15 - position 2
T=15 - position 3

(stack positions from base)

A is pushed to the top and colour changed to grey as it's the ref base, GT are ordered alpha as same value.  It would be nice to have a mouse over that gives total read depth and count+fraction of each base.  A plugin that extends the existing alignements2 to add the ability to select a 'stack' display mode in the track menu would be how I'd anticipate this working.

I may do something similar with multibigwig but that will involve generating 4 additional BigWig files.  It would be very fast but not as good for identifying locations of non-ref change.

Thoughts?

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: Allele column from BAM?

Suzanna Lewis-3
I don't currently know of any track like that, but I strongly second this request.

I had originally (before your email) been thinking of a sequence logo type display when fully zoomed in, but using the 4-color stacks with the height of each color(base) proportionate to its frequency would achieve the same effect at a lower zoom level.

For population data, that provides the overall background frequency for each base, I have a pretty good idea of what I'd like to see for this when zoomed out. Here what is interesting/useful isn't which base it is, but rather where things are conserved or not. Ten(for example) possible lines/bins/slots each corresponding to a percentage range. When frequency of one allele is >90% then that slot/bin is filled in. So highly conserved regions would all be on the same line or just a narrow band of lines, whereas variable regions would be more scattered across the slots. It would give a quick visual on where things are highly conserved.

In any case, just wanted to say this is on the radar.

-S


On Fri, Aug 19, 2016 at 3:00 AM, Keiran Raine <[hidden email]> wrote:
Hi,

Does anyone know of a plugin that could produce a fixed height track which gives a fractional ACGT colour based stack for each position?

We generate deep sequence amplicon data and need a way to display the data using less screen real estate, but I see this as generally useful for Alignment tracks.

What I'd ideally be looking for is a track that would stack from most prevelant non-ref base and switch the colour for the ref base to grey.

e.g.

REF = A
Reads:
A=50 - position 4
C=30 - position 1
G=15 - position 2
T=15 - position 3

(stack positions from base)

A is pushed to the top and colour changed to grey as it's the ref base, GT are ordered alpha as same value.  It would be nice to have a mouse over that gives total read depth and count+fraction of each base.  A plugin that extends the existing alignements2 to add the ability to select a 'stack' display mode in the track menu would be how I'd anticipate this working.

I may do something similar with multibigwig but that will involve generating 4 additional BigWig files.  It would be very fast but not as good for identifying locations of non-ref change.

Thoughts?

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: Allele column from BAM?

Keiran Raine
Hi Suzanna,

We have an unstacked version working from BigWig: https://github.com/elsiklab/multibigwig/issues/8#issuecomment-242336208

(we've also written the C code to generate the input files efficiently from BAM/CRAM)

I'm working on a plugin based on MultiBigWig to take this and stack the bars right now:


I'll keep the list posted once I have a working version

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 25 Aug 2016, at 20:43, Suzanna Lewis <[hidden email]> wrote:

I don't currently know of any track like that, but I strongly second this request.

I had originally (before your email) been thinking of a sequence logo type display when fully zoomed in, but using the 4-color stacks with the height of each color(base) proportionate to its frequency would achieve the same effect at a lower zoom level.

For population data, that provides the overall background frequency for each base, I have a pretty good idea of what I'd like to see for this when zoomed out. Here what is interesting/useful isn't which base it is, but rather where things are conserved or not. Ten(for example) possible lines/bins/slots each corresponding to a percentage range. When frequency of one allele is >90% then that slot/bin is filled in. So highly conserved regions would all be on the same line or just a narrow band of lines, whereas variable regions would be more scattered across the slots. It would give a quick visual on where things are highly conserved.

In any case, just wanted to say this is on the radar.

-S


On Fri, Aug 19, 2016 at 3:00 AM, Keiran Raine <[hidden email]> wrote:
Hi,

Does anyone know of a plugin that could produce a fixed height track which gives a fractional ACGT colour based stack for each position?

We generate deep sequence amplicon data and need a way to display the data using less screen real estate, but I see this as generally useful for Alignment tracks.

What I'd ideally be looking for is a track that would stack from most prevelant non-ref base and switch the colour for the ref base to grey.

e.g.

REF = A
Reads:
A=50 - position 4
C=30 - position 1
G=15 - position 2
T=15 - position 3

(stack positions from base)

A is pushed to the top and colour changed to grey as it's the ref base, GT are ordered alpha as same value.  It would be nice to have a mouse over that gives total read depth and count+fraction of each base.  A plugin that extends the existing alignements2 to add the ability to select a 'stack' display mode in the track menu would be how I'd anticipate this working.

I may do something similar with multibigwig but that will involve generating 4 additional BigWig files.  It would be very fast but not as good for identifying locations of non-ref change.

Thoughts?

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank" class="">+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: Allele column from BAM?

Suzanna Lewis-3
Super Keiran!

Looking forward to seeing it!


On Thu, Aug 25, 2016 at 1:00 PM, Keiran Raine <[hidden email]> wrote:
Hi Suzanna,

We have an unstacked version working from BigWig: https://github.com/elsiklab/multibigwig/issues/8#issuecomment-242336208

(we've also written the C code to generate the input files efficiently from BAM/CRAM)

I'm working on a plugin based on MultiBigWig to take this and stack the bars right now:


I'll keep the list posted once I have a working version

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 25 Aug 2016, at 20:43, Suzanna Lewis <[hidden email]> wrote:

I don't currently know of any track like that, but I strongly second this request.

I had originally (before your email) been thinking of a sequence logo type display when fully zoomed in, but using the 4-color stacks with the height of each color(base) proportionate to its frequency would achieve the same effect at a lower zoom level.

For population data, that provides the overall background frequency for each base, I have a pretty good idea of what I'd like to see for this when zoomed out. Here what is interesting/useful isn't which base it is, but rather where things are conserved or not. Ten(for example) possible lines/bins/slots each corresponding to a percentage range. When frequency of one allele is >90% then that slot/bin is filled in. So highly conserved regions would all be on the same line or just a narrow band of lines, whereas variable regions would be more scattered across the slots. It would give a quick visual on where things are highly conserved.

In any case, just wanted to say this is on the radar.

-S


On Fri, Aug 19, 2016 at 3:00 AM, Keiran Raine <[hidden email]> wrote:
Hi,

Does anyone know of a plugin that could produce a fixed height track which gives a fractional ACGT colour based stack for each position?

We generate deep sequence amplicon data and need a way to display the data using less screen real estate, but I see this as generally useful for Alignment tracks.

What I'd ideally be looking for is a track that would stack from most prevelant non-ref base and switch the colour for the ref base to grey.

e.g.

REF = A
Reads:
A=50 - position 4
C=30 - position 1
G=15 - position 2
T=15 - position 3

(stack positions from base)

A is pushed to the top and colour changed to grey as it's the ref base, GT are ordered alpha as same value.  It would be nice to have a mouse over that gives total read depth and count+fraction of each base.  A plugin that extends the existing alignements2 to add the ability to select a 'stack' display mode in the track menu would be how I'd anticipate this working.

I may do something similar with multibigwig but that will involve generating 4 additional BigWig files.  It would be very fast but not as good for identifying locations of non-ref change.

Thoughts?

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.


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