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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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No chromosome Y data for genocluster and LRR/BAF- Affy Axiom data #50

Open Melb1 opened 4 years ago

Melb1 commented 4 years ago

Hi there

I am generating genocluster followed by LogRR/BAF on Axiom PMDA data. It working for all chromosomes but not for Y and we are particularly interested in Chr Y. The pfb file has annotation for all chr Y probes ?

any idea why this is happening?

kaichop commented 4 years ago

You need to generate PFB file yourself, from your own array data.

On Tue, Nov 19, 2019 at 3:29 PM Melb1 notifications@github.com wrote:

Hi there

I am generating genocluster followed by LogRR/BAF on Axiom PMDA data. It working for all chromosomes but not for Y and we are particularly interested in Chr Y. The pfb file has annotation for all chr Y probes ?

any idea why this is happening?

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Melb1 commented 4 years ago

How i can generate the pfb file?

kaichop commented 4 years ago

compile_pfb.pl can be used

On Tue, Nov 19, 2019 at 3:43 PM Melb1 notifications@github.com wrote:

How i can generate the pfb file?

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Melb1 commented 4 years ago

can you please provide me a link where i can find the detail of compile_pfb.pl,

kaichop commented 4 years ago

You are asking the question on the github repository that hosted PennCNV.

https://github.com/WGLab/PennCNV

On Tue, Nov 19, 2019 at 3:51 PM Melb1 notifications@github.com wrote:

can you please provide me a link where i can find the detail of compile_pfb.pl,

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Melb1 commented 4 years ago

Thanks, i know about github repository for compile_pfb.pl, but need to know the example to use it, like what input files etc.

Melb1 commented 4 years ago

Anyother issue is compile.pfb aspet B allele freq file and I do not have chr Y probes in B allele freq files?

kaichop commented 4 years ago

Just run it and it will tell you how to use it, like any other command in penncnv.

On Tue, Nov 19, 2019 at 3:59 PM Melb1 notifications@github.com wrote:

Thanks, i know about github repository for compile_pfb.pl, but need to know the example to use it, like what input files etc.

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kaichop commented 4 years ago

you should first learn how to use penncnv, understand all the basics such as how to run a command and how to interpret results, there are online tutorials that give step by step instructions. Do not use GitHub Issue for asking questions.

On Tue, Nov 19, 2019 at 4:20 PM Melb1 notifications@github.com wrote:

Anyother issue is compile.pfb aspet B allele freq file and I do not have chr Y probes in B allele freq files?

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Melb1 commented 4 years ago

okay thanks, sorry for confusion but it says aspect B allele freq file and I do not have chr Y probes in B allele freq files?

kaichop commented 4 years ago

What does " aspect B allele freq file" mean? I do not have any idea. What is "it" in "it says"?

Did you check with whoever provided you with the data why there is no chrY probe in BAF file, and why you want to have chrY CNV calls from a file that has no chrY markers? It could be that only CN markers are provided in chrY but even if so, these markers should still be in BAF file typically.

Again, read the tutorials, FAQs, instructions, etc, and run the example commands first, to get some basic understanding of PennCNV, before digging into more advanced topics.

On Tue, Nov 19, 2019 at 4:34 PM Melb1 notifications@github.com wrote:

okay thanks, sorry for confusion but it says aspect B allele freq file and I do not have chr Y probes in B allele freq files?

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