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