PARP-1 interacting snoRNA and DDX21

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

• spike_in_correlation.py: Script to look at Spike-in counts to correlation
• spike_in_correlation.sh: Script to analyze spike-ins
• RNA-seq.Rmd: RNA-seq of data analysis regardless of spike-ins

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