Installation
The latest version is available here: Download, then unzip:tar zxvf ChangePoint-x.x.x.tar.gzTesting
Run the following command:perl path/to/change_point.pl -t treatment.bam
-c normal.bam -g 3utr.bed -d s -o outputFor some systems that bedtools could not be running properly, users may need to download and recompile it and replace bedtools and intersectBed in ChangePoint/bin. Also see more details about output in Manual.Input bams: treatment.bam , normal.bam Regions: 3utr.bed Analysis type: shortening Output file: output.rlts.txt Number of reads threshold: 20 Level for mdFDR: 0.05 Hypothesized odds ratio: 2 Min heap size for JVM: 256m Max heap size for JVM: 1024m [16/7/2013 18:12:2] Start analysis... [16/7/2013 18:12:2] Processing alignments... [16/7/2013 18:12:13] Sorting files... [16/7/2013 18:12:42] Preparing input data... [16/7/2013 18:12:45] Detecting change point for each region... [16/7/2013 18:13:9] Performing addtional fisher's exact test... [16/7/2013 18:13:10] Removing intermediate files... [16/7/2013 18:13:10] Finished.