Welcome to the CTX-Explorer app.
This open-source Python 3 program was developed for identification of inter- and intrachromosomal translocations.
Additional Python libraries that need to be installed for this app to work correcly: subprocess, re, os, gzip, sys, getopt, statistics, itertools, termcolor
Additional software that needs to be installed for this app to work correctly: samtools, bamtools
The following options are available:
-h, --help: prints this help message.
-t, --threads: defines the number of CPU threads that are to be used (default: 1).
-T, --tmpdir: defines the directory where temporary files are to be stored (default: current dir).
-q, --qual: defines the minimal Phred quality score of mappings to be used (default: 20).
-b, --bamfile: the name of a BAM file to be used (MANDATORY).
-I, --intractx: indicates if intra-chromosomal translocations should be evaluated (default: 'no'). This option significantly increases memory usage.
-1, --chrom1: the name of the first chromosome (optional) involved in a translocation (e.g., 'chr1').
-2, --chrom2: the name of the second chromosome (optional) involved in a translocation (e.g., 'chr2').
-l, --tlen: minimal distance (in nucleotides) between the first and the second read forming a read pair (default: 1,000,000).
-i, --insert: the maximum insert size used for identification of CTX-supporting reads and hit pairs (default: median insert size * 2).
-n, --nohits: minimal number of hits for a translocation to be stored in the final report (default: 2).
-N, --nohits_sec: minimal number of hits per the second chromosome for a translocation to be stored in the final report (default: 2).
-s, --min_size: minimal size of a hit group for a translocation to be stored in the final report (default: 2).
-d, --no_filter: specifies whether the filtering by the number of supporting reads should be turned off (default: 'no').
-p, --prefix: specifies a prefix of a file in which the final report will be saved (default: 'output').
-g, --gzipped: indicates whether the final report file should be gzipped (default: 'no').
-v, --version: prints the version of this program.