Commit 82f7c5b7 authored by María Morales Martínez's avatar María Morales Martínez
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proyecto test1

parent 44a46ab2
# Histone marks distribution in chromatin beds
# Histone marks distribution in chromatin beds (IN CONSTRUCTION)
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This pipeline is dedicated to estimate the tendency of histone marks (or other possible transcription factor) in different established regions along the nuclei. Chromatin extension is divided acording to radial "artificial" regions from the periphery (Lamin) to center of the nuclei and statistics from the distribution of each acetylation/methylation mark in those regions are calculated (mean and std). These regions are defined by their distances that moves away to Lamin B1 protein.
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......@@ -18,10 +18,14 @@ List of chip-seq bed files that are going been used to check the chromatin. Grac
#### Input Chromatin Bed
Chromatin input bed must be storage in */data/chromatin_bed/[category]/* (created by you).
Chromatin input bed must be storage in */data/target_bed/[category]/* (created by you).
Establishing different categories avoid mix different types of bed files.
### Input Hi-C
**Not inclueded in this example**
### Installation
This tool is programmed under python==3.7.8.
......@@ -46,7 +50,7 @@ Execute the following command adding the required information for the arguments.
python run_smk.py [-h] -c CONFIG -s SMK
```
- **Configuration (CONFIG)**: Input file with all the parametters required to run the pipeline: type or regions in chromatin to contrast (chromatin_category), bed in side of this category to be analysed, histone chip-seq dataset with all samples, list of histone chip-seq to use in the analysis.Save new config file (".json") in config folder.
- **Configuration (CONFIG)**: Input file with all the parametters required to run the pipeline: type or regions in chromatin to contrast (target_category), bed in side of this category to be analysed, histone chip-seq dataset with all samples, list of histone chip-seq to use in the analysis.Save new config file (".json") in config folder.
- **Snakemake workflow (SMK)**: snake file with the description of the workflow followed by rules that determine the order of data processing. Placed in sanakemake folder.
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