creating a chainfile for plant species

[Brown, Anne - ARS]

Hello,

 

I am looking to create a chainfile from version1 to version2 of the soybean reference genome. I would also like to be able to easily convert coordinate positions between older assembly versions and future versions of the soybean reference genome. I have tried looking at the tutorials on how to create a chainfile but all of the tutorials use small genomes. I am wondering if you could help me create a chainfile for soybean or if there is a way you can do it for us if we provide you with the 2 assemblies? Please let me know.

Thank you,

 

Anne Brown

Research Biologist

 

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[Hiram Clawson]

Good Afternoon Dr. Brown:

I'm wondering if the assemblies you are referring to are any
of these refseq assemblies:

GCF_000004515.1_V1.0 # Date: 2010-1-11
GCF_000004515.2_V1.0 # Date: 2012-9-7
GCF_000004515.3_V1.1 # Date: 2012-9-7
GCF_000004515.4_Glycine_max_v2.0 # Date: 2015-11-4

Or these genbank assemblies:

GCA_000004515.1_V1.0 # Date: 2010-1-11
GCA_000004515.2_V1.1 # Date: 2012-9-7
GCA_000004515.3_Glycine_max_v2.0 # Date: 2015-11-4
GCA_001269945.1_Glycine_max_Enrei_1.0 # Date: 2015-7-4
GCA_001269945.2_Glycine_max_Enrei_2.0 # Date: 2015-8-6
GCA_002905335.1_glyma.Lee.gnm1 # Date: 2018-1-30

Can you confirm the sequence size of these assemblies is less 1 billion bases ?

--Hiram

[Hiram Clawson]

Good Morning Anne:

This fits in with some work I'm doing to get our tool chains
independent of our environment here. Let me take a look at
this today.

--Hiram

On 4/13/18 8:16 AM, Brown, Anne - ARS wrote:
> Hi Hiram,
>
> Thank you for the fast response. Yes, I am interested in a chainfile from:
> GCF_000004515.3_V1.1 to GCA_000004515.3_Glycine_max_v2.0
> GCA_000004515.3_Glycine_max_v2.0 to GCA_002905335.1_glyma.Lee.gnm1
> And GCF_000004515.3_V1.1 to GCA_002905335.1_glyma.Lee.gnm1
>
> All of these assemblies are less than 1 billion bases.
>
> Anne Brown,

[Brown, Anne - ARS]

Hi Hiram,

Thank you for the fast response. Yes, I am interested in a chainfile from:
GCF_000004515.3_V1.1 to GCA_000004515.3_Glycine_max_v2.0
GCA_000004515.3_Glycine_max_v2.0 to GCA_002905335.1_glyma.Lee.gnm1
And GCF_000004515.3_V1.1 to GCA_002905335.1_glyma.Lee.gnm1

All of these assemblies are less than 1 billion bases.

Anne Brown,