Setup

First,bowtie2 and bedtools must be installed and accessible from the terminal.

Additionally, large files with experimental data used in this project are hosted on GitHUB LFS server. To be able to pull this project you must follow the instructions to install LFS extension for git.

When Above dependencies are satisfied you can run following code from command line to install the rest of dependencies.

git pull [email protected]:brainbreaks/DSB_Paper.git
cd DSB_Paper
python3 -m pip install genome_downloader
python3 -m genome_downloader mm10 genomes
git pull [email protected]:brainbreaks/breaktools.git
RScript 00-setup.R

Related to Repli-SEQ -> OK-Seq termination zones (ignore for now)

Tables

Data	Source	Celltype	Treatment	Organism	Processed
HTGTS	Wei PNAS 2018	NPC	APH / DMSO	Mouse	Yes
HTGTS	Tena PNAS 2018	NPC, ESC	APH / DMSO	Mouse	Yes
HTGTS	Tena PNAS 2018	NPC, ESC	APH / DMSO	Mouse	Yes
HTGTS	Wang Cell 2020	NPC	APH / DMSO	Human	No
HTGTS	HTGTS	NPC	APH (0.2-0.6) / DMSO	Mouse	Partial
HTGTS	HTGTS-genes	NPC -genes*	APH / DMSO	Mouse	Yes
HTGTS	HTGTS_inverse	NPC inverse gene*	APH / DMSO	Mouse	N/A
RepliSeq	Zhao GeneBio 2020	NPC, ESC	DMSO	Mouse	Yes
RepliSeq	RepSeq-1	NPC	APH (4frac) / DMSO (8frac)	Mouse	Yes
RepliSeq	RepSeq-2	NPC	APH (8frac+) / DMSO (8frac+)	Mouse	N/A
OK-seq	Petric	ESC	DMSO	Mouse	Yes
GROseq	GROseq	ESC	DMSO???	Mouse	Yes

##Hypothesis We want to prove that one of the reasons for RDC formation is head-on collission from replication and transcription forks

##Plan

1. Continue collecting TLX files
2. Find replication termination sites
3. Use

  graph TD;
      repliseq_zhao[(RepliSeq<br>Zhao)]--data ESC-->tts_model;
      okseq_petric[(OK-seq<br>Petric)]--labels ESC-->tts_model;
      tts_model[TTS model]--predict-->tts_prediction[TTS prediction];
      repliseq_vivien2[RepliSeq<br>Vivien]--data-->tts_prediction[TTS prediction];
      htgts[(HTGTS<br/>0.5 Aph)]--Compare breaks:<br>head-on vs chasing-->collision[Head-on<br>collision];
      tts_prediction-->collision{Head-on<br>collision};
      
      

Loading

#repliseq_zhao[(RepliSeq
Zhao)]--data NPC-->repliseq_zhao[(RepliSeq
Zhao)];

  #id4[TTS]-->id5{TTS enrichment}
  C-->D;

*TTS - Transcription termination site ()