Closed DrFakhar closed 1 year ago
DrFakhar
commented
1 year ago which file should i use for illumina arrays? https://github.com/WGLab/PennCNV/blob/master/affy/libgw5/agre.hmm Or https://github.com/WGLab/PennCNV/blob/master/affy/libgw6/affygw6.hmm Or anyother?
kaichop
commented
1 year ago I asume you are asking about the hmm file (not the pfb). Generally speaking if you are using an Illumina array, you can just use the hhall.hmm file. The "affygw6" and "agre" were originally created for Affymetrix arrays.
On Thu, Jul 20, 2023 at 4:54 AM DrFakhar @.***> wrote:
Closed #111 https://github.com/WGLab/PennCNV/issues/111 as completed.
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DrFakhar
commented
1 year ago Thank you for your response.
From where i can download the hhall.hmm file. Kindly guide
Thank you in advance Fakhar
On Mon, Jul 24, 2023 at 7:11 AM Kai Wang @.***> wrote:
I asume you are asking about the hmm file (not the pfb). Generally speaking if you are using an Illumina array, you can just use the hhall.hmm file. The "affygw6" and "agre" were originally created for Affymetrix arrays.
On Thu, Jul 20, 2023 at 4:54 AM DrFakhar @.***> wrote:
Closed #111 https://github.com/WGLab/PennCNV/issues/111 as completed.
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kaichop
commented
1 year ago It is part of PennCNV package.
On Mon, Jul 24, 2023 at 12:22 AM DrFakhar @.***> wrote:
Thank you for your response.
From where i can download the hhall.hmm file. Kindly guide
Thank you in advance Fakhar
On Mon, Jul 24, 2023 at 7:11 AM Kai Wang @.***> wrote:
I asume you are asking about the hmm file (not the pfb). Generally speaking if you are using an Illumina array, you can just use the hhall.hmm file. The "affygw6" and "agre" were originally created for Affymetrix arrays.
On Thu, Jul 20, 2023 at 4:54 AM DrFakhar @.***> wrote:
Closed #111 https://github.com/WGLab/PennCNV/issues/111 as completed.
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DrFakhar
commented
1 year ago Thank you so much.
Now i need your guidance regarding the preparation of gc model file Bostaurus 1.9 assembly. Can you please share me the link of gc content file.
On Mon, 24 Jul 2023, 17:45 Kai Wang, @.***> wrote:
It is part of PennCNV package.
On Mon, Jul 24, 2023 at 12:22 AM DrFakhar @.***> wrote:
Thank you for your response.
From where i can download the hhall.hmm file. Kindly guide
Thank you in advance Fakhar
On Mon, Jul 24, 2023 at 7:11 AM Kai Wang @.***> wrote:
I asume you are asking about the hmm file (not the pfb). Generally speaking if you are using an Illumina array, you can just use the hhall.hmm file. The "affygw6" and "agre" were originally created for Affymetrix arrays.
On Thu, Jul 20, 2023 at 4:54 AM DrFakhar @.***> wrote:
Closed #111 https://github.com/WGLab/PennCNV/issues/111 as completed.
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kaichop
commented
1 year ago No need to use gc model unless your data is of very low quality.
On Mon, Jul 24, 2023 at 8:58 AM DrFakhar @.***> wrote:
Thank you so much.
Now i need your guidance regarding the preparation of gc model file Bostaurus 1.9 assembly. Can you please share me the link of gc content file.
On Mon, 24 Jul 2023, 17:45 Kai Wang, @.***> wrote:
It is part of PennCNV package.
On Mon, Jul 24, 2023 at 12:22 AM DrFakhar @.***> wrote:
Thank you for your response.
From where i can download the hhall.hmm file. Kindly guide
Thank you in advance Fakhar
On Mon, Jul 24, 2023 at 7:11 AM Kai Wang @.***> wrote:
I asume you are asking about the hmm file (not the pfb). Generally speaking if you are using an Illumina array, you can just use the hhall.hmm file. The "affygw6" and "agre" were originally created for Affymetrix arrays.
On Thu, Jul 20, 2023 at 4:54 AM DrFakhar @.***> wrote:
Closed #111 https://github.com/WGLab/PennCNV/issues/111 as completed.
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DrFakhar
commented
1 year ago That is great.
Thank you so much.
On Mon, 24 Jul 2023, 18:04 Kai Wang, @.***> wrote:
No need to use gc model unless your data is of very low quality.
On Mon, Jul 24, 2023 at 8:58 AM DrFakhar @.***> wrote:
Thank you so much.
Now i need your guidance regarding the preparation of gc model file Bostaurus 1.9 assembly. Can you please share me the link of gc content file.
On Mon, 24 Jul 2023, 17:45 Kai Wang, @.***> wrote:
It is part of PennCNV package.
On Mon, Jul 24, 2023 at 12:22 AM DrFakhar @.***> wrote:
Thank you for your response.
From where i can download the hhall.hmm file. Kindly guide
Thank you in advance Fakhar
On Mon, Jul 24, 2023 at 7:11 AM Kai Wang @.***> wrote:
I asume you are asking about the hmm file (not the pfb). Generally speaking if you are using an Illumina array, you can just use the hhall.hmm file. The "affygw6" and "agre" were originally created for Affymetrix arrays.
On Thu, Jul 20, 2023 at 4:54 AM DrFakhar @.***> wrote:
Closed #111 https://github.com/WGLab/PennCNV/issues/111 as completed.
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I am working on SNP Chip data of cattle genome. I have made the .pfb file. From where to download the .hall file for my dataset? i am unable to find any download link?
Sorry in advance, if its a childish question.