SAM file directionality

Understanding direction flags and how to extract them

• http://biobeat.wordpress.com/2013/03/14/separating-bam-files-to-forward-and-reverse-strand-files/
• http://biobeat.wordpress.com/2013/04/29/directional-rna-seq-part-1-extract-strand-information-from-sam-file/

 Paired-end specific discussion:

• http://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/
• http://www.novocraft.com/wiki/tiki-index.php?page=Extracting+unmapped+reads+from+a+BAM+file+produced+by+novoalign

Useful samflag utility
http://picard.sourceforge.net/explain-flags.html