LiftOver literature?

[Yuncheng Duan]

Hi,

Is there any official literature introducing liftOver algorithms and files? (I've been looking at genomewiki - liftOver how to). just wondered if there's any recommended material for me to understand liftOver.

Thanks a lot,

Yuncheng

[Daniel Schmelter]

Hello Yuncheng,

Thank you for using the Genome Browser and writing in to learn more about LiftOver.

Here is a list of our resources and a publication on that topic. The publication is not about LiftOver itself, it is on our chain/net alignment algorithm which produces chain files that are at the base of the LiftOver tool. Here is a paper on our chains/net generation program:

https://www.pnas.org/content/100/20/11484

Since you've already seen the LiftOver How-To wiki, you might find the following documentation helpful:

http://genomewiki.ucsc.edu/index.php/How_Liftover_Works
https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Liftover
http://genome.sph.umich.edu/wiki/LiftOver
https://genome.ucsc.edu/FAQ/FAQdownloads.html#download28
http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver

This content can be quite confusing, so for specific questions, you may also be interested in our question and answer archive:

https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/liftOver

I encourage you to reach again if you have any specific questions after reviewing the documentation. Please reply-all to genome...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,
Daniel Schmelter
UCSC Genomics Institute

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAOyni9tw5xzgpqvKhZ1DGS1uv2kZvcY1b%3DNhgnfqbZUN4G%3DjXA%40mail.gmail.com.

[Michael Hiller]

Dear UCSC team, 

we have a multiple alignment (maf) that includes for several species more than one assembly. 

E.g. mouse mm10 and mm39. 

However, the hgTrackUi generated track page only shows 'mouse', which I assume is automatically fetched from dbDb, since the the trackDb entry lists something like

sGroup_Rodentia mm10 mm39

Also, the actual browser page (hgTracks) shows only 'mouse', which makes it hard to distinguish between these assemblies in the browser.

What we would like to do is to show both the species name + the assembly name, 

e.g. mouse_mm10 mouse_mm39

Is there a chance to implement this in the browser code ?

I believe there must be a place where the browser translates the assembly name from trackDb.ra to the species name, where the assembly name can simply be added. 

If you could point me to where in the code the 'right' place is, we can give it a try ourselves. 

Thanks a lot

- Michael 

-- 

Michael Hiller, PhD

Professor of Comparative Genomics
LOEWE Centre for Translational Biodiversity Genomics,
Senckenberg Society for Nature Research & Goethe University, 

Frankfurt am Main, Germany

[Brian Raney]

I can add this as an option in trackDb.   Who doesn't love new trackDb variables?

Thanks for the suggestion Michael.  This will probably make it into the Dec 14 release of v424

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu.

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/499B7947-E3A3-4B67-988C-51CB9182C532%40senckenberg.de.

[Brian Raney]

Sure, we'll do that. What do you think about being able to specify
the labels through a trackDb variable that maps sequence names to
labels? That would give developers full control over the labels.

On Fri, Nov 12, 2021 at 1:34 AM Michael Hiller
<michael...@senckenberg.de> wrote:
>
> Hi Brian,
>
> that would be awesome.
> Can you pls give me a heads up when we can pull the new code.
>
> Thanks a bunch.
> - Michael

>
> On 11. Nov 2021, at 21:34, Brian Raney <bra...@soe.ucsc.edu> wrote:
>
> I can add this as an option in trackDb. Who doesn't love new trackDb variables?
>
> Thanks for the suggestion Michael. This will probably make it into the Dec 14 release of v424
>
> On Thu, Nov 11, 2021 at 8:44 AM Michael Hiller <michael...@senckenberg.de> wrote:
>>
>> Dear UCSC team,
>>
>> we have a multiple alignment (maf) that includes for several species more than one assembly.
>> E.g. mouse mm10 and mm39.
>>

>> <PastedGraphic-3.tiff>

>>
>> However, the hgTrackUi generated track page only shows 'mouse', which I assume is automatically fetched from dbDb, since the the trackDb entry lists something like
>> sGroup_Rodentia mm10 mm39
>>
>> Also, the actual browser page (hgTracks) shows only 'mouse', which makes it hard to distinguish between these assemblies in the browser.

>> <PastedGraphic-4.tiff>

[Michael Hiller]

Hi Brian, 

that sounds like a great idea, especially as for most mafs 'just' having the species names would be fully sufficient. 

Thanks a bunch

- Michael 

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAKNgKOJtjkRw4%2B%2Bww3Ces-B4W0WjUYJ%2B1O0M8wamWVQKy0C8Fw%40mail.gmail.com.

[Michael Hiller]

Hi Brian, 

that would be awesome. 

Can you pls give me a heads up when we can pull the new code. 

Thanks a bunch. 

- Michael 

On 11. Nov 2021, at 21:34, Brian Raney <bra...@soe.ucsc.edu> wrote:

I can add this as an option in trackDb.   Who doesn't love new trackDb variables?

Thanks for the suggestion Michael.  This will probably make it into the Dec 14 release of v424

On Thu, Nov 11, 2021 at 8:44 AM Michael Hiller <michael...@senckenberg.de> wrote:

Dear UCSC team, 

we have a multiple alignment (maf) that includes for several species more than one assembly. 

E.g. mouse mm10 and mm39. 

<PastedGraphic-3.tiff>

However, the hgTrackUi generated track page only shows 'mouse', which I assume is automatically fetched from dbDb, since the the trackDb entry lists something like

sGroup_Rodentia mm10 mm39

Also, the actual browser page (hgTracks) shows only 'mouse', which makes it hard to distinguish between these assemblies in the browser.

<PastedGraphic-4.tiff>

What we would like to do is to show both the species name + the assembly name, 

e.g. mouse_mm10 mouse_mm39

Is there a chance to implement this in the browser code ?

I believe there must be a place where the browser translates the assembly name from trackDb.ra to the species name, where the assembly name can simply be added. 

If you could point me to where in the code the 'right' place is, we can give it a try ourselves. 

Thanks a lot

- Michael 

-- 

Michael Hiller, PhD

Professor of Comparative Genomics
LOEWE Centre for Translational Biodiversity Genomics,
Senckenberg Society for Nature Research & Goethe University, 

Frankfurt am Main, Germany

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/499B7947-E3A3-4B67-988C-51CB9182C532%40senckenberg.de.