Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

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 scripture
-------------------- /usr/local/Modules/3.2.9/modulefiles ----------------------
scripture

$ module load scripture

$ module list
Currently Loaded Modulefiles:
  1) scripture

$ module unload scripture

$ module show scripture  # this actually show graphviz module since it's used to view output of scripture.
-------------------------------------------------------------------
/usr/local/Modules/3.2.9/modulefiles/scripture:

module-whatis    Sets up graphviz v2.28 
prepend-path     PATH /usr/local/graphviz-2.28.0_el5/bin 
prepend-path     LD_LIBRARY_PATH /usr/local/graphviz-2.28.0_el5/  
-----------------------------------------------------------------

Example

See http://www.broadinstitute.org/software/scripture/Walkthrough_example for detail

$ module load scripture
$ module load igvtools
$ mkdir /data/$USER/scripture; cd /data/$USER/scripture
$ ln -s /spin1/db/genome/mm9/chr19.fa chr19
$ gunzip GSE20851_GSM521650_ES.aligned.sam.gz
$ igvtools index GSE20851_GSM521650_ES.aligned.sam
$ java -jar /usr/local/scripture-beta2.jar -alignment /data/$USER/scripture/GSE20851_GSM521650_ES.aligned.sam \
-out chr19.scriptureESTest.segments -sizeFile /usr/local/apps/scripture/mm9.sizes -chr chr19 \
-chrSequence /fdb/genome/mm9/chr19.fa
$ java -jar /usr/local/scripture-beta2.jar -task extractDot -in chr19.scriptureESTest.segments.dot \
-chr chr19 -start 32165265 -end 32455031 -out sgms1.dot
$ ......

Documentation

http://www.broadinstitute.org/software/scripture/Walkthrough_example