Changes between Version 68 and Version 69 of SOPs/mapping

Timestamp:

08/25/20 15:27:52 (5 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -19 +19 @@
 The [[http://bio-bwa.sourceforge.net/ | Burrows-Wheeler Alignment (BWA) tool]] 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 (up to 100 bp) reads:''
+''Sample commands for short (up to 100 nt) reads:''
 {{{
 # Align single-end reads
@@ -32 +32 @@
 Use "-n" option to change the maximum number of mismatches in the alignment.
 
-''Sample commands for long (70bp or longer) reads:''
+''Sample commands for long (70 nt or longer) reads:''
 {{{
 # Align single-end reads
@@ -38 +38 @@
 # Align paired-end reads
 bsub "bwa mem /nfs/genomes/sgd_2010/bwa/sacCer3.fa Reads.1.fq Reads.2.fq > Mapped_reads.bwa.sam"
+}}}
+
+And then convert the SAM to BAM, sort, and index.  This BaRC script can to all three with one command.  (Then the original SAM can be deleted.)
+
+{{{
+/nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl input.sam
 }}}