README.md 987 Bytes
Newer Older
1
2
3
4
PARP-1 interacting snoRNA and DDX21
=================================

## External Data used in analysis:
Venkat Malladi's avatar
Venkat Malladi committed
5
6
- reference_annotations: Reference annotations of coding and noncoding transcripts
    - parse_annotations.sh: Script to breakdown annotations
7

Venkat Malladi's avatar
Venkat Malladi committed
8
## Requirements:
9
10
11
- bedtools v2.25.0
- UCSC tools
- bedops v2.2.14
Venkat Malladi's avatar
Venkat Malladi committed
12
13
14
15
16
17
18
19
20
21
- 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
    
22
23
24

## Analysis of RIP-seq data
- RIP-seq.Rmd: Analysis of RIP-seq data
Venkat Malladi's avatar
Venkat Malladi committed
25
26
- figures/: Figures related to RIP-seq binding
- tables/: Tables of RIP-seq binding
27
28
29
30
31
32
33
34

## 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