Installation

The latest version is available here: Download, then unzip:

tar zxvf EBChangePoint_x.x.x.tar.gz

Testing

Run the following command:

perl path/to/EBChangePoint.pl -c control.bam -t case.bam -g exon.bed -h1 junctions_control.bed -h2 junctions_case.bed -o Output.txt

If successful, you should see the following:

Input bams: case.bam , control.bam

Regions: exon.bed

Output file: Output.txt

Level for mdFDR: 0.05

Min heap size for JVM: 256m

Max heap size for JVM: 1024m

Control junction file: junctions_control.bed. Junction supported positions are considered as hot points.

Case junction file: junctions_case.bed. Junction supported positions are considered as hot points.

[13/5/2015 3:28:36] Start analysis...

[13/5/2015 3:28:36] Processing alignments...

[13/5/2015 3:28:43] Sorting files...

[13/5/2015 3:28:47] Count number of reads in each exon...

[13/5/2015 3:28:48] Compute junction spans...

[13/5/2015 3:28:50] Prepare data...

[13/5/2015 3:29:6] Detecting change points...

Optimization and parameters estimation for control data set (P, r, alpha, beta, weight):

...

Optimization and parameters estimation for case data set (P, r, alpha, beta, weight):

...

[13/5/2015 3:35:35] Report final results under designed FDR level...

[13/5/2015 3:35:36] Removing intermediate files...

[13/5/2015 3:35:37] Finished.

For some systems that bedtools could not be running properly, users may need to download and recompile it and replace bedtools and intersectBed in EBChangePoint/bin.

Also see more details about output in Manual.