ep_cmdline.pl generates scripts that call JBD. It provides
good default arguments and an easy way to specify non-default
arguments. The simplest invocation would be from the directory
containing your datafiles and is
ep_cmdline.pl --dir .
ep_cmdline.pl will do the following things:
Since ep_cmdline.pl generates calls to the jbd program you compiled, it needs to know the path to your matlab installation and the jbd program. You'll need to edit the $jbdpath variable to tell it where to find the jbd binary. You may also need to help it find matlab. You will also probably need to modify the lines that generate LD_LIBRARY_PATH for the scripts, depending on the architecture that you're using.
You might need to modify ep_cmdline.pl if you're using a job-queueing
system other than PBS/Torque or if it can't find your matlab
installation. JBD can take a while to run, depending on how much data
you have (in terms of number of probes and number of replicates) and
also depending on the data itself. Some data is harder to deconvolve
than other. One input parameter that makes a big difference is
minboundy. If JBD can't find a ratio greater than this
value, it won't look find binding in a region. We use 1.4 as the
default value, which gives a good tradeoff between speed and sensitivity
to smaller binding events. Higher values will examine fewer regions,
thus yielding shorter runtimes but potentially missing more binding events.