X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=erange.git;a=blobdiff_plain;f=docs%2FREADME.rna-seq;h=605c48592359b6fefe129cd1e945fa624e7d6a3c;hp=5a866f31a7e2a0ece21a116751263e60a771401c;hb=0d3e3112fd04c2e6b44a25cacef1d591658ad181;hpb=5e4ae21098dba3d1edcf11e7279da0d84c3422e4

diff --git a/docs/README.rna-seq b/docs/README.rna-seq
index 5a866f3..605c485 100644
--- a/docs/README.rna-seq
+++ b/docs/README.rna-seq
@@ -117,7 +117,7 @@ python $ERANGEPATH/combineRPKMs.py
 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.
 
@@ -141,11 +141,11 @@ In alternative 1, we use reads that did not match an existing gene
 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, 
@@ -212,9 +212,9 @@ convert it into the format that cistematic expects using
 
 $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>
 
@@ -256,6 +256,7 @@ in README.rna-esnp .
 
 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