This repository contains scripts associated with the analysis of data created with the Cergentis TLA technology
The methods and protocols to which the scripts in this repository belong are described in:
M. Z. Alimohamed, L. F. Johansson, E. N. De Boer, E. Splinter, P. Klous, M. Yilmaz, A. Bosga, M. Van Min, A. B. Mulder, E. Vellenga, R. J. Sinke, R. H. Sijmons, E. Van Den Berg, and B. Sikkema-Raddatz, “Genetic screening test to detect translocations in acute leukemias by use of targeted locus amplification,” Clin. Chem., vol. 64, no. 7, 2018.
The scripts used in the paper were submitted in this repository on 26 Apr 2017 (commit 6c83b09)
##Dependencies and used scripts The script splitfqbyCATG.pl can be found on https://gist.github.com/mmterpstra/2417200a96f841862c82220893490202
The script in remove_duplicates_from_fastq.py was created by Pengfei Yu and can also be copied from https://www.biostars.org/p/2733/
The Regions_of_interest.txt file should have the following format. Tab delimited. First column gene name; second column chr:start-stop. For instance:
RUNX1 21:36150098-36421595
The scripts "windowed_coverage.pl", "in_silico_enrich.pl" and "human-mouse_singleGenomePlot_normalized.R" have been created by Cergentis B.V.
Cergentis B.V.
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The file human-mouse_singleGenomePlot_normalized_fix_20160920_abscut100_Inhousefiltered.R is an adaptation of the human-mouse_singleGenomePlot_normalized.R script. The following changes are made:
Function removeSmall:
n <- names(cnt[cnt >= 0]) is changed to n <- names(cnt[cnt > 100])
Function translocationPlot:
abs.cut <-3 is changed to abs.cut <-100
Added lines to section "#remove 'chr' string"
# remove chr names that contain "GL"
td <- td[grep("GL",td[,1], invert=T),]
# remove chr names that contain "25"
td <- td[grep("25",td[,1], invert=T),]
Changed in section " # check if chrY exists"
if(sum(chroms == 'chrY')){ is changed to if(sum(chroms == 'chr24')){
td[td[,1]=='X',1] <- length(chroms)-1 is changed to td[td[,1]=='chr23',1] <- length(chroms)-1 td[td[,1]=='Y',1] <- length(chroms) is changed to td[td[,1]=='chr24',1] <- length(chroms) td[td[,1]=='X',1] <- length(chroms) is changed to td[td[,1]=='chr23',1] <- length(chroms)
###Further dependencies: cutadapt (v1.8.1): https://pypi.python.org/pypi/cutadapt
samtools (v1.2 and v1.3): http://www.htslib.org/
bwa (v0.7.12): http://bio-bwa.sourceforge.net/
Perl (v5.22.0): https://www.perl.org/
R (V3.2.2 or higher): https://www.r-project.org/