Changes between Version 23 and Version 24 of SOPs/mapping

Timestamp:

08/05/15 10:32:11 (9 years ago)

Author:

thiruvil

Comment:

--

SOPs/mapping

@@ -60 +60 @@
 Bwa is a software package containing several related algorithms using the Burrows-Wheeler Transform.  It works well even with indels, but not with spliced (RNA) reads. 
 
-Sample commands for short (upto 100 bp) reads:
+''Sample commands for short (upto 100 bp) reads:''
 {{{
 # Align single-end reads
@@ -71 +71 @@
 }}}
 
-Sample commands for long (70bp or longer) reads:
+Use "-n" option to change the maximum number of mismatches in the alignment.
+
+''Sample commands for long (70bp or longer) reads:''
 {{{
 # Align single-end reads
@@ -79 +81 @@
 }}}
 
+For aligning long reads using the bwa mem option, there's no maximum number of mismatches, this is analogous to a local alignment using blat/blast.
+
+[[BR]]
+
 '''Other tools'''
-
 Many other regular mapping tools are also available, although they generally require a tool-specific indexed version of the genome.