Scripts for Center for Functional Genomics HPC:

Demux, QC and Utilities

bcl2fastq.HPC.sh:
        Demultiplexes Illumina NextSeq 500 samples (bcl intensities to fastq).
        Performs quality control assessments using FASTQC. 
        Generates a single html report plotting all quality control metrics.

    Usage: 
        $ sbatch bcl2fastq.HPC.sh NameOfRunFolder NameOfSampleSheet NameOfPI 

barcodeSplit.pl: 
    Demultiplexes fastq reads based on barcodes of interest.

reHash.py:
    Rename utility.

reveRse.py:
    Generates i5 reverse complements for Illumina NextSeq 500 samples. 
    
    Usage: 
        $ python reveRse.py < indices.txt >

RNA-seq

star.align.HPC.sh: 
        Aligns PE or SE fastq samples to reference genome using star ultrafast aligner. 
        Generates bedgraph files for UCSC genome browser visualization. 
    
    Usage: 
        $ sbatch star.align.HPC.sh <SE or PE> <ORG> <ASSEMBLY> 

DESeq2.R:
    Performs differential gene expression analysis of RNA-seq samples. 
    (rawCounts used are either from STAR --quantMode GeneCounts or HTSEQ outputs)
    
    Usage: 
        $ RScript DESeq2.R <Experiment.Name> <Numerator> <Denominator>
    
    For DESeq2 processCounts.sh and countMatrix.sh helper scripts are available for 
    preprocessing raw counts and creating the countMatrix.txt file, needed by the DESeq2.R script. 
    
    Usage: 
    $ processCounts.sh <1> or <2>

CHIP-seq

MACS

DeepTools