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 ## 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