and get back a version number and all possible command line options:
version 1.0
-usage: python $ERANGEPATH/combineRPKMs.py firstRPKM expandedRPKM finalRPKM combinedOutfile [-withmultifraction]
+usage: python $ERANGEPATH/combineRPKMs.py firstRPKM expandedRPKM finalRPKM combinedOutfile [--withmultifraction]
where fields in brackets are optional.
model to identify candidate regions:
# Alternative 1: find new regions outside of gene models with reads piled up
-python $ERANGEPATH/findall.py RNAFAR LHCN10213.rds LHCN10213.newregions.txt -RNA -minimum 1 -nomulti -flag NM -log rna.log -cache 1
+python $ERANGEPATH/findall.py RNAFAR LHCN10213.rds LHCN10213.newregions.txt --RNA --minimum 1 --nomulti --flag NM --log rna.log --cache 1
# Alternative 1: filter out new regions that overlap repeats more than a certain fraction
# use "none" if you don't have a repeatmask database
-python $ERANGEPATH/checkrmask.py ../hg19repeats/rmask.db LHCN10213.newregions.txt LHCN10213.newregions.repstatus LHCN10213.newregions.good -log rna.log -startField 1 -cache 1
+python $ERANGEPATH/checkrmask.py ../hg19repeats/rmask.db LHCN10213.newregions.txt LHCN10213.newregions.repstatus LHCN10213.newregions.good --log rna.log --startField 1 --cache 1
In alternative 2, we pool multiple RNA-seq datasets into a single
RDS database, run it through the two scripts of alternative 1 above,
$ERANGEPATH/gfftocis.py infile.gff outfile.cis
-NOTE THAT YOU WILL MOST LIKELY HAVE TO EDIT THIS FILE TO
-ACCOMODATE YOUR SPECIFIC GFF FORMAT TO THE CISTEMATIC
-FORMAT, WHICH IS
+NOTE THAT THIS FILE IS PROVIDED AS AN EXAMPLE ONLY. YOU WILL MOST
+LIKELY HAVE TO EDIT THIS FILE TO ACCOMODATE YOUR SPECIFIC GFF
+FORMAT TO THE CISTEMATIC FORMAT, WHICH IS
geneID<tab>uniqRef<tab>chrom<tab>start<tab>stop<tab>sense<tab>type<return>
RELEASE HISTORY
+version 3.3 November 2010 - updated command line options
version 3.2 December 2009 - support for custom genome annotations with Cistematic 3.0
version 3.1 April 2009 - modified normalizeFinalExonic.py to remove genome
version 3.0 January 2009 - added logging to shell pipelines