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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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PFB file for Illumina GSA array #35

Closed Taylor95 closed 5 years ago

Taylor95 commented 5 years ago

Hi Dr Wang, Thanks for your time. I am generating a PFB file for Illumina GSA array from my signal files. Here's the command:

compile_pfb.pl -listfile sampleID.txt -output try.pfb

The files look as follows:

Name Chr Position GType B Allele Freq Log R Ratio 1:100292476 1 100292476 AA 0.00 0.1172143 1:101064936 1 101064936 AA 0.01691524 0.06694419

The following are the outputs that are produced when run the command:

NOTICE: A total of 2267 input signal files is specified in sampleID.txt NOTICE: File handle cannot be created by the operating system after reading 1021 files NOTICE: The B Allele Freq information is annotated as column 5 in input files NOTICE: A total of 1021 input files will be used for compiling PFB values

Are there too much input files? I have thousands of signal files. How to handle this? BTW, Do i just need control's signal files or pool cases and controls together when i compile my own PFB file?

Thank you!

kaichop commented 5 years ago

Your operating system only supports 1024 files. If you have root access, you can use ulimit command to increase the limit, otherwise, using only 1021 files is good enough to create the PFB file. You can just use the existing PFB file.

On Tue, Jan 1, 2019 at 8:48 PM Yaqian1995 notifications@github.com wrote:

Hi Dr Wang, Thanks for your time. I am generating a PFB file for Illumina GSA array from my signal files. Here's the command:

compile_pfb.pl -listfile sampleID.txt -output try.pfb

The files look as follows:

Name Chr Position GType B Allele Freq Log R Ratio 1:100292476 1 100292476 AA 0.00 0.1172143 1:101064936 1 101064936 AA 0.01691524 0.06694419

The following are the outputs that are produced when run the command:

NOTICE: A total of 2267 input signal files is specified in sampleID.txt NOTICE: File handle cannot be created by the operating system after reading 1021 files NOTICE: The B Allele Freq information is annotated as column 5 in input files NOTICE: A total of 1021 input files will be used for compiling PFB values

Are there too much input files? I have thousands of signal files. How to handle this? BTW, Do i just need control's signal files or pool cases and controls together when i compile my own PFB file?

Thank you!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/35, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuEtFM0jwqb9Wb9ySvanHo_UCc1Hfks5u_A_YgaJpZM4ZmHx2 .

Taylor95 commented 5 years ago

OK, thanks for answering my question!

————————

Yaqian Liu School of Public Health Nanjing Medical University

On 1/2/2019 12:26，Kai Wangnotifications@github.commailto:notifications@github.com wrote： Your operating system only supports 1024 files. If you have root access, you can use ulimit command to increase the limit, otherwise, using only 1021 files is good enough to create the PFB file. You can just use the existing PFB file.

On Tue, Jan 1, 2019 at 8:48 PM Yaqian1995 notifications@github.com wrote:

Hi Dr Wang, Thanks for your time. I am generating a PFB file for Illumina GSA array from my signal files. Here's the command:

compile_pfb.pl -listfile sampleID.txt -output try.pfb

The files look as follows:

Name Chr Position GType B Allele Freq Log R Ratio 1:100292476 1 100292476 AA 0.00 0.1172143 1:101064936 1 101064936 AA 0.01691524 0.06694419

The following are the outputs that are produced when run the command:

NOTICE: A total of 2267 input signal files is specified in sampleID.txt NOTICE: File handle cannot be created by the operating system after reading 1021 files NOTICE: The B Allele Freq information is annotated as column 5 in input files NOTICE: A total of 1021 input files will be used for compiling PFB values

Are there too much input files? I have thousands of signal files. How to handle this? BTW, Do i just need control's signal files or pool cases and controls together when i compile my own PFB file?

Thank you!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/35, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuEtFM0jwqb9Wb9ySvanHo_UCc1Hfks5u_A_YgaJpZM4ZmHx2 .

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/WGLab/PennCNV/issues/35#issuecomment-450785440, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AsJj9-9RoQVFIzj_kfRoyhdjdtwVhONcks5u_DT7gaJpZM4ZmHx2.

ejh243 commented 5 years ago

following on from this what is a reasonable number of samples to create a pfb file?

kaichop commented 5 years ago

at least 100, ideally 1000.

On Wed, May 8, 2019 at 7:16 AM ejh243 notifications@github.com wrote:

following on from this what is a reasonable number of samples to create a pfb file?

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haydeeartaza commented 4 years ago

Your operating system only supports 1024 files. If you have root access, you can use ulimit command to increase the limit, otherwise, using only 1021 files is good enough to create the PFB file. You can just use the existing PFB file. … On Tue, Jan 1, 2019 at 8:48 PM Yaqian1995 @.***> wrote: Hi Dr Wang, Thanks for your time. I am generating a PFB file for Illumina GSA array from my signal files. Here's the command: compile_pfb.pl -listfile sampleID.txt -output try.pfb The files look as follows: Name Chr Position GType B Allele Freq Log R Ratio 1:100292476 1 100292476 AA 0.00 0.1172143 1:101064936 1 101064936 AA 0.01691524 0.06694419 The following are the outputs that are produced when run the command: NOTICE: A total of 2267 input signal files is specified in sampleID.txt NOTICE: File handle cannot be created by the operating system after reading 1021 files NOTICE: The B Allele Freq information is annotated as column 5 in input files NOTICE: A total of 1021 input files will be used for compiling PFB values Are there too much input files? I have thousands of signal files. How to handle this? BTW, Do i just need control's signal files or pool cases and controls together when i compile my own PFB file? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#35>, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuEtFM0jwqb9Wb9ySvanHo_UCc1Hfks5u_A_YgaJpZM4ZmHx2 .

Hi, where can I find this pfb file?

kaichop commented 4 years ago

PFB is specific for each array type. You can create a PFB file if you have a few hundred signal intensity files.

santoroml commented 4 years ago

Hi, can I use my target data to generate the pfb file or do I need to use an independent sample?

kaichop commented 4 years ago

okay to use your target data to generate pfb.

On Tue, Mar 3, 2020 at 9:49 PM PGTunifesp notifications@github.com wrote:

Hi, can I use my target data to generate the pfb file or do I need to use an independent sample?

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