Intersection

[Firebird]

Hello,

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

Thanks

[nickloman]

I like to import such data into R and use the set manipulation functions e.g.

http://stat.ethz.ch/R-manual/R-patched/library/base/html/sets.html

[nickloman]

Another way is to write Python scripts and use the sets library:

http://docs.python.org/library/sets.html

[Firebird]

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

[doc.ramses]

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.

[colindaven]

You can also try Galaxy. I've found it very useful for set manipulation via a web browser.

[Firebird]

@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