Fgf15 FACS

Analyzing genes changed with diet in Fgf15-positive cells from ileum.

Files

+-- data
    +-- Run_2425
        +-- Sample_113433
            +-- ReadsPerGene.out.tab
        +-- Sample_113434
            +-- ReadsPerGene.out.tab
        +-- ...
        +-- Run_2425_seeley.csv
    +-- Run_2643
        +-- Sample_123057
            +-- ReadsPerGene.out.tab
        +-- Sample_123058
            +-- ReadsPerGene.out.tab
        +-- ...
        +--
        +-- Run_2643_seeley.csv
    +-- genes.csv
+-- scripts
    +-- analysis.R
    +-- mapping.sh
+-- environment.yml
+-- README.md

Pipeline

Setup

1. Create anaconda environment: conda env create -f environment.yml
2. Activate anaconda environment: conda activate Fgf15

Analysis

1. Map FASTQ files: bash scripts/map.sh (note this does not work in the GitHub repo because FASTQ files are not included).
2. Analyze count files: Rscript scripts/analyze.R

Results

All results found in the results folder

• results.csv: numeric results from analysis pipeline
• kegg.csv: KEGG enrichment results
• plots/kegg.png: figure from the paper