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Venkat Malladi authored
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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