Computing ChIP-seq coverage of replication timing quantiles - Bash and R scripts
| Main Author: | Bellani, Marina A. |
|---|---|
| Other Authors: | Seidman, Michael M. |
| Format: | info software Journal |
| Bahasa: | eng |
| Terbitan: |
, 2020
|
| Online Access: |
https://zenodo.org/record/3875101 |
Daftar Isi:
- BASH scripts process.sh process2.sh Divide the genome into genomic windows of a specified size, calculate the mean replication timing (RT) score (or eigenvector score) for each window, compute the coverage of each ChIP-seq BAM file for each genomic window and generate a table [forR.BL.ok.tab] displaying CHIP-seq coverage per genomic window for the different samples (and removes blacklisted regions and "chrUn|chrEBV|chrY|random|\s.\s"). R scripts Functions TMP-per_RTquantile -Data import [ forR.BL.ok.tab ] -Data wrangling -Conversion of coverage data into Tags per million using toTMP function -Calculates for each sample ‘Coverage in TPM per RT (or eigenvector) quantile’ using convertToQuantiles function -Generates a box plot of TMP per RT quantile for all samples -Saves the sets of box plots as a png file
- This research was supported, in part, by the Intramural Research Program of the NIH, National Institute on Aging, United States (Z01-AG000746-08).