Changes between Version 17 and Version 18 of SOPs/mapping

Timestamp:

01/31/14 11:14:24 (11 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -119 +119 @@
   * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
   * '''--segment-length <int>'''  Shortest length of a spliced read that can map to one side of the junction.  For reads shorter than ~45 nt, set this to half the read length (so set '--segment-length 20' for 40-nt reads).  For longer reads, the default length (25) can be used.
-  * '''-I <int>''' Maximum intron length.  If your genome has introns that are all shorter (or often longer) than the default value (500000), set this to a more appropriate value.
+  * '''-I <int>''' Maximum intron length.  If your genome has introns that are all shorter (or many that are longer) than the default value (500000), set this to a more appropriate value.
   * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
   * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.