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jkimlab / DESCHRAMBLER

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per-chromosome chain file with two species #15

Closed DustinSokolowski closed 1 year ago

DustinSokolowski commented 1 year ago

Hey!

I have assembled a de novo rodent genome and I'm looking to compute genome-wide syntenic blocks to the mm10. With only a two species tree, do I need to have the chain and net file split by each chromosome for both my genome and mm10, or does just my genome suffice?

Best, Dustin

jkimlab commented 1 year ago

Hi Dustin,

If you just want to build synteny blocks, I recommend one of the following tools.

GMASS: https://github.com/jkimlab/GMASS

mySyntenyPortal: https://github.com/jkimlab/mySyntenyPortal

In those tools, you don’t need to worry about chain/net files. You just need to provide assembly sequence files.

Thanks.

On Jul 21, 2023, at 3:44 AM, Dustin Sokolowski @.***> wrote:

Hey!

I have assembled a de novo rodent genome and I'm looking to compute genome-wide syntenic blocks to the mm10. With only a two species tree, do I need to have the chain and net file split by each chromosome for both my genome and mm10, or does just my genome suffice?

Best, Dustin

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/15, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV4JVEEMSP7VEUXR3E3XRF4ALANCNFSM6AAAAAA2R2WE5I. You are receiving this because you are subscribed to this thread.

DustinSokolowski commented 1 year ago

Hey,

Thank you for the quick response, and I'm sorry about my unfamiliarity with your excellent software, I think I'm going to be changing that very soon.

What I'm looking to do is take about 100 candidate tandem duplication regions (100Kb-1Mb) in my genome and visualize the synteny between species with a linear synteny view. The original plan was to use the output of DESCHRAMBLER with syntenyPlotteR to generate these plots in a high-throughput manner.

image

If I were to use GMASS, would the CSB/ directory contain the analogous output files to look at these syntenic plots in a high throughput manner?

jkimlab commented 1 year ago

I don’t know about syntenyPlotteR, so I don’t know it can work with GMASS.

But if you use mySyntenyPortal, you can create a similar webpage as shown below.

http://bioinfo.konkuk.ac.kr/synteny_portal/htdocs/synteny_browser.php?whole_spc=hg38_mm39&chr=chr1&resolution=150000

On Jul 21, 2023, at 12:10 PM, Dustin Sokolowski @.***> wrote:

Hey,

Thank you for the quick response, and I'm sorry about my unfamiliarity with your excellent software, I think I'm going to be changing that very soon.

What I'm looking to do is take about 100 candidate tandem duplication regions (100Kb-1Mb) in my genome and visualize the synteny between species with a linear synteny view. The original plan was to use the output of DESCHRAMBLER with syntenyPlotteR to generate these plots in a high-throughput manner.

https://user-images.githubusercontent.com/56414662/255058698-e6a9af31-be48-4f6a-9682-3a37e583a81e.png If I were to use GMASS, would the CSB/ directory contain the analogous output files to look at these syntenic plots in a high throughput manner?

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/15#issuecomment-1644923691, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV3X65QDF6WGBG5BZLDXRHXJBANCNFSM6AAAAAA2R2WE5I. You are receiving this because you commented.

DustinSokolowski commented 1 year ago

Hey,

These look beautiful, though I didn't know mySyntenyPortal functioned with a custom reference based on the paper. Is there new documentation that allows for this? My assembly is currently on rapid-ensembl and not yet UCSC, so I'm not sure if it's compatible.

Best! Dustin

jkimlab commented 1 year ago

mySyntenyPortal works with any assembly files. Just prepare two fasta files for each of the assemblies you want to compare, and specify their paths in the parameter file of mySyntenyPortal. Please check the Github page.

On Jul 21, 2023, at 12:40 PM, Dustin Sokolowski @.***> wrote:

Hey,

These look beautiful, though I didn't know mySyntenyPortal functioned with a custom reference based on the paper. Is there new documentation that allows for this? My assembly is currently on rapid-ensembl and not yet UCSC, so I'm not sure if it's compatible.

Best! Dustin

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/15#issuecomment-1644939973, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV6XVV3ADSRJ5RCDOGLXRH227ANCNFSM6AAAAAA2R2WE5I. You are receiving this because you commented.

DustinSokolowski commented 1 year ago

Great, I see this now. Thanks so much!

Dustin