Changes between Version 26 and Version 27 of SOPs/miningSAMBAM

Timestamp:

02/04/15 09:18:13 (10 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -3 +3 @@
 Many of these involve [http://samtools.sourceforge.net/samtools.shtml samtools]
 
+=== Get the official SAM/BAM file format description  ===
+
+All fields in a SAM/BAM file are explained in the [http://samtools.github.io/hts-specs/SAMv1.pdf Sequence Alignment/Map Format Specification].
+
 === Convert, sort, and/or index ===
-
 
 {{{
@@ -104 +107 @@
 # read_ID<tab>read<tab>number times mapped
 }}}
+
+=== SAM flag explanation ===
+
+   * An explanation of all flags is found in the [http://samtools.github.io/hts-specs/SAMv1.pdf Sequence Alignment/Map Format Specification].
+   * Converting a flag into its components may be easiest with the Picard [https://broadinstitute.github.io/picard/explain-flags.html Explain SAM Flags] tool.
 
 === QC to get a (visual) summary of mapping statistics.  For eg. coverage/distribution of mapped reads across the genome or transcriptome. ===