ChIP-seq

Collection of small programs to be used for ChIP-seq analysis.

count_chip_peaks

This program serves to find genes that are bound by PBX1 in several locations. To find respective genes, the annotations to both strands are used and saved in two separate output dicionaries.

Input: .csv file of PBX1 ChIP-Seq peaks

Output: Dictionary, counting the number of peaks for each gene that are bound by PBX1 is listed.

Author: Vera Laub

Last edited: 2019-12-03

randomized_peak_shift

This script serves to construct randomized peak shifts for ChIP-seq peaks.

Input: ChIP-seq peaks in .bed (.txt), mouse data

Output:

1. Cleaned input file (removed random peaks that are not on chr1-19, X or Y) in .bed (or .txt)
2. Randomly shifted ChIP-seq peaks in .bed (.txt)

Note on implementation: Ideally, script should not only be applied once but multiple (e.g. 1000x?) times, in order to compute randomized background and followed by overlap with bedtools intersect

Author: Vera Laub

Last Edited: 2022-11-09

chip-seq_rna-seq_peak_collection

This program serves the purpose of assembling Genes from an RNA-seq file (1. Input) and collecting the respective ChIP-seq peaks (2. Input), i.e. PBX1 ChIP-seq peaks of genes that are differentially regulated in Pbx1 kd RNA-seq in aNS cells (but can be used on any kind of ChIP/RNA-seq, if necessary data is provided). Code meant to be flexible :)!

Input: .txt with RNA-Seq data (ENSEMBLE ID, Gene ID, Fold change), .txt files with ChIP-seq data (Gene ID, peak chr, peak start, peak stop, summit chr, summit start, summit stop)

Output: .bed files with ChIP-seq peaks of all genes defined in RNA-seq file (peak chr, peak start, peak stop, Gene ID); peaks for up/downregulated genes are saved in separate files; whole peaks and 200nt summit of peaks saved in separate files for subsequent analysis

Author: Vera Laub

Last Edited: 2023-02-20