MuG - CHi-C Pipeline
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Table of Contents
Requirements and Installation
Full Installation
Pipelines
Tools for processing fastq C-HiC files
Architectural Design Record
License
MuG - CHi-C Pipeline
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Documentation for CHi-C Pipeline
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Documentation for CHi-C Pipeline
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Table of Contents
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Requirements and Installation
Requirements
Installation
Full Installation
Setup the System Environment
Setup pyenv and pyenv-virtualenv
Installation Process
Setup the symlinks
Prepare the Python Environment
Pipelines
Map and parse CHi-C reads
Create CHiCAGO input RMAP
Create CHiCAGO input BAITMAP
Create CHiCAGO input Design files
Convert BAM file into chicago input files .chinput
Data normalization and peak calling
Run the entire CHi-C pipeline
Tools for processing fastq C-HiC files
Map and parser reads
Create CHiCAGO input files
Convert bam files into chicago input
Normalize data and call C-HiC peaks
Architectural Design Record
25-09-2018 handling_chr_header branch merge with master
15-10-2018 mm_mods_for_makebaitmaps branch merge with master
License
Indices and tables
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Index
Module Index
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