LAM-HTGTS

Containing Scripts for LAM-HTGTS data analysis

Call TranslocPreprocess.pl in your terminal in the format as followings

TranslocPreprocess.pl path_to/metadata.txt path_to_preprocess/ --read1 path_to_sequence_file/Library_Run_Name.R1.fastq.gz --read2 path_to_sequence_file/Library_Run_Name.R2.fastq.gz

For advanced usage, TranslocPreprocess.pl --help

Call TranslocPreprocess.pl in the following format

TranslocWrapper.pl path_to/metadata.txt preprocess/ results/ --threads N

For advanced usage, TranslocWrapper.pl --help

Call JoinT.R in the following format

path_to/JoinT.R path_to/meta.txt path_to/preprocess_folder/ path_to/result_folder/ path_to/output_directory/

For advanced usage, JoinT.R --help

the metadata should be constructed as for rejoin, i.e. with these columns:

Library Sequencing Researcher Assembly Chr Start End Strand Breakseq Breaksite MID Primer Adapter Cutter 5nt_BaitEnd 5nt_PreyStart Amplicon Description

Usage of tlx2bed.py as followings

tlx2bed.py [-h] -f TLXFILE [-o OUTPREFIX] [-t {bed,both,bedgraph}] [-g {mm9,hg19,hg38,mm10}] [--v3]

The function of tlxbedintersect.py depends on two other scripts, tlx2BED.pl and pullTLXFromBED.pl.

Usage: python tlxbedintersect.py path_to/directory_with_tlx_files path_to/region_of_interest.bed

Call tlx2BED-MACS.pl in the following format

tlx2BED-MACS.pl path_to/result_or_final_tlx Name_Of_New_File.bed

Call JctStructure.R in the following format

JctStructure.R path_to/meta.txt path_to/folder_with_tlx_files extension_of_the_files nb_max_of_MH_insertion

Call ResectionRSS.R in the following format

ResectionRSS.R path_to/meta.txt path_to/folder_with_results_from_tlxbed_intersect path_to/bedfile.bed extension_of_the_files