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Old 07-05-2013, 07:37 AM   #1
nickschurch
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Default Switch strands of a bam file...

I have a bam file where the strand information has been unintentionally reversed. Is there an easy command in samtools for switching the strand information for every read? If not, what is the best way to do this? I guess I could loop though each read in python and switching the bit flag, but I really don't want to have to code this myself if there is a better (read faster) solution...
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Old 07-05-2013, 08:54 PM   #2
sdriscoll
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I don't know of any standard tool that will do this. Code!
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/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
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Old 07-08-2013, 07:21 AM   #3
nickschurch
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problem solved:

https://pypi.python.org/pypi?name=ng...action=display
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