PARP-1 interacting snoRNA and DDX21
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## External Data used in analysis:
- reference_annotations: Reference annotations of coding and noncoding transcripts
    - parse_annotations.sh: Script to breakdown annotations

## Requirements:
- bedtools v2.25.0
- UCSC tools
- bedops v2.2.14
- RSEM 1.2.31


## Miscellaneous
- misc: Test code never used
    - gene_matrix.sh: Generate gene matrix using RSEM
    - fpkm.py: Take average FPKM of replicates
    - diff_genes.sh: EBseq differential gene analysis
    - rip_seq_rna_seq_analysis.py: Using STAR to analyze RIP-seq data


## Analysis of RIP-seq data
- RIP-seq.Rmd: Analysis of RIP-seq data
- figures/: Figures related to RIP-seq binding
- tables/: Tables of RIP-seq binding

## Analysis of RNA-seq


## General Analysis
- Summary_RIP-seq.xlsx: Summary of RIP-seq sequencing data bound RNA types
- Summary_RNA-seq.xlsx: Summary of RNA-seq for DDX21 perturbations
- Figures.pptx: Powerpoint of Figures
- reference_annotations: Reference annotations files
- ERCC_spikein: ERCC 92 spikein information