README.md 1.25 KB
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
- 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
Venkat Malladi's avatar
Venkat Malladi committed
21

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

## Analysis of RNA-seq
Venkat Malladi's avatar
Venkat Malladi committed
29
- spike_in_correlation.py: Script to look at Spike-in counts to correlation
30
31
32
- spike_in_correlation.sh: Script to analyze spike-ins
- RNA-seq.Rmd: RNA-seq of data analysis regardless of spike-ins

33
34
35
36
37
38


## 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
Venkat Malladi's avatar
Venkat Malladi committed
39
40
- reference_annotations: Reference annotations files
- ERCC_spikein: ERCC 92 spikein information