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