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Ruitulyu / KAS-Analyzer

New computational framework to process and analyze KAS-seq and spKAS-seq data.
MIT License
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Peakscalling documentation is incorrect #12

Closed ecroot closed 12 months ago

ecroot commented 12 months ago

Describe the bug The README file (https://github.com/Ruitulyu/KAS-Analyzer/blob/main/README.md) documents use of the -t argument for input in peakscalling, but it is not valid (running peakscalling with the -t option causes the error 'illegal option -t').

The documentation at https://ruitulyu.github.io/KAS-Analyzer/ correctly documents the use of -k for input files. However, it does not document calling peaks individually (only for replicates), despite the fact that individual peaks files are required by other steps of the tool.

To Reproduce see the section 'call KAS-seq peaks with KAS-seq data individually' at https://github.com/Ruitulyu/KAS-Analyzer/blob/main/README.md , and the section 'peakscalling' at https://ruitulyu.github.io/KAS-Analyzer/

Expected behavior Correct, complete documentation of the command in all locations

Ruitulyu commented 12 months ago

Thanks! The -t arguments in script and documentation have been corrected. Best, Ruitu

On Mon, Nov 27, 2023 at 8:36 AM E Croot @.***> wrote:

Describe the bug The README file ( https://github.com/Ruitulyu/KAS-Analyzer/blob/main/README.md) documents use of the -t argument for input in peakscalling, but it is not valid (running peakscalling with the -t option causes the error 'illegal option -t').

The documentation at https://ruitulyu.github.io/KAS-Analyzer/ correctly documents the use of -k for input files. However, it does not document calling peaks individually (only for replicates), despite the fact that individual peaks files are required by other steps of the tool.

To Reproduce see the section 'call KAS-seq peaks with KAS-seq data individually' at https://github.com/Ruitulyu/KAS-Analyzer/blob/main/README.md , and the section 'peakscalling' at https://ruitulyu.github.io/KAS-Analyzer/

Expected behavior Correct, complete documentation of the command in all locations

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ecroot commented 12 months ago

Thanks!