Rseg on Helix
The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3.
NOTE: Related rseg files have been downloaded under /fdb/rseg
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
$ module avail rseg -------------------- /usr/local/Modules/3.2.9/modulefiles ---------------------- rseg/0.4.4 rseg/0.4.7 rseg/0.4.8(default) $ module load rseg $ module list Currently Loaded Modulefiles:
1) rseg/0.4.8 $ module unload rseg $ module load rseg/0.4.7 $ module show rseg ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/rseg/0.4.8: module-whatis Sets up rseg 0.4.8 prepend-path PATH /usr/local/apps/rseg/0.4.8/bin prepend-path LD_LIBRARY_PATH /usr/local/gsl-x86_64/lib -----------------------------------------------------------------
How To Use
$ module load rseg $ cd /data/$USER/rseq $ rseg -c /fdb/rseg/XXX.bed -o /data/$USER/rseg/out -i 20 -v /data/$USER/fileName
