X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=erange.git;a=blobdiff_plain;f=docs%2FREADME.rnapath;fp=docs%2FREADME.rnapath;h=8a35232a1f8d84ff2baafe2cfb98e8ff9320d6cc;hp=c64579b2f206c8ec8fe47c4027261ba5fe284072;hb=0d3e3112fd04c2e6b44a25cacef1d591658ad181;hpb=5e4ae21098dba3d1edcf11e7279da0d84c3422e4

diff --git a/docs/README.rnapath b/docs/README.rnapath
index c64579b..8a35232 100644
--- a/docs/README.rnapath
+++ b/docs/README.rnapath
@@ -37,13 +37,14 @@ the list of paired reads that do not map to the same contig. This involves
 specifying a distance to distalPairs.py that is greater than the length of the 
 largest existing genomic contig. For example:
 
-python ../commoncode/distalPairs.py 20000 rna_on_genomic.rds rna_on_genomic.crosspairs -splices -cache 20000000
+python ../commoncode/distalPairs.py 20000 rna_on_genomic.rds rna_on_genomic.crosspairs --splices --cache 20000000
 
 4. RUNNING RNAPATH.py
 
-You can now run RNAPATH.py. I suggest optionallly using the included script processvelvet.py to rename the contigs, before running blat and generating the crosspair data.
+You can now run RNAPATH.py. I suggest optionally using the included script processvelvet.py to rename the contigs, before running blat and generating the crosspair data.
 
 Example: $ERANGEPATH/rnapath/RNAPATH.py genomic_contigs.fa rna_on_genomic.crosspairs RNAPATH.log genome.RNAPATH.fa
 
-version 3.2    May  2010 - first release
+version 3.3    November 2010 - updated command line options
+version 3.2    May      2010 - first release