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Old 01-11-2011, 06:50 AM   #1
Firebird
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Default Intersection

Hello,

I want to do an intersection of several exomes to find common mutations in these exomes. How can I do that?

Thanks
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Old 01-11-2011, 07:37 AM   #2
nickloman
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I like to import such data into R and use the set manipulation functions e.g.
http://stat.ethz.ch/R-manual/R-patch...html/sets.html
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Old 01-11-2011, 07:41 AM   #3
nickloman
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Another way is to write Python scripts and use the sets library:
http://docs.python.org/library/sets.html
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Old 01-18-2011, 06:30 AM   #4
Firebird
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I am not good either in R or in Python. Is there maybe a command line tool I can use? My data is in .tab format.

Thank you
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Old 01-18-2011, 08:01 AM   #5
doc.ramses
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The easiest way for non-bioinformatics is to do this is in MS Access. There you can generate relationship based queries. E.g. column chromosome from table 1 has to match column chromosome from table 2 and column chromosome position from table 1 has to match column chromosome position from table 2.
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Old 01-19-2011, 01:16 AM   #6
colindaven
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You can also try Galaxy. I've found it very useful for set manipulation via a web browser.
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Old 01-19-2011, 07:57 AM   #7
Firebird
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@doc.ramses: I tried it with Excel, but I'll check out Acess.

@colindaven: I also use galaxy, nice website btw. Which feature can I use for intersection. Can you may tell me the workflow?

Thanks
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