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Old 09-27-2013, 02:42 AM   #1
shadow19c
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Location: france

Join Date: Oct 2012
Posts: 27
Default Samtools: Mapped reads and unmapped reads

Hello,
I have a problem and I don't understand the flag number to extract alignment.

So my question is I want to extract from a bowtie alignment all the reads if one mapped and the other does'nt map to do a CV analysing after.

I want only unmmaped reads if one pair mapped properly only.

I tried -f 3 -F 260
and -f 4 -F 264 but it does not give me what i want, if anyone can help me.




------- ----------
Map Unmapped

or

------- ----------
Unmapped Map

Thank you very much
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Old 09-27-2013, 02:57 AM   #2
paolo.kunder
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Location: Milano, Italy

Join Date: Aug 2011
Posts: 92
Default

this link may help you:

http://picard.sourceforge.net/explain-flags.html

maybe you are interested in -f 8
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