Samtools: Mapped reads and unmapped reads

[shadow19c]

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

[paolo.kunder]

this link may help you:

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

maybe you are interested in -f 8