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PARP-1 interacting snoRNA and DDX21
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## External Data used in analysis:
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- reference_annotations: Reference annotations of coding and noncoding transcripts
    - parse_annotations.sh: Script to breakdown annotations
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## Requirements:
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- bedtools v2.25.0
- UCSC tools
- bedops v2.2.14
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- 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
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## Analysis of RIP-seq data
- RIP-seq.Rmd: Analysis of RIP-seq data
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- figures/: Figures related to RIP-seq binding
- tables/: Tables of RIP-seq binding
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## Analysis of RNA-seq
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- spike_in_correlation.py: Script to look at Spike-in counts to correlation
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- spike_in_correlation.sh: Script to analyze spike-ins
- RNA-seq.Rmd: RNA-seq of data analysis regardless of spike-ins

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## 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
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- reference_annotations: Reference annotations files
- ERCC_spikein: ERCC 92 spikein information