Intersection

Firebird · 01-11-2011, 06:50 AM

Hello,

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

Thanks

nickloman · 01-11-2011, 07:37 AM

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

nickloman · 01-11-2011, 07:41 AM

Another way is to write Python scripts and use the sets library:
http://docs.python.org/library/sets.html

Firebird · 01-18-2011, 06:30 AM

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 · 01-18-2011, 08:01 AM

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 · 01-19-2011, 01:16 AM

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

Firebird · 01-19-2011, 07:57 AM

@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

01-11-2011, 06:50 AM	#1
Firebird Member Location: Germany Join Date: Jun 2010 Posts: 18	Intersection Hello, I want to do an intersection of several exomes to find common mutations in these exomes. How can I do that? Thanks

01-11-2011, 07:37 AM	#2
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	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

01-11-2011, 07:41 AM	#3
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	Another way is to write Python scripts and use the sets library: http://docs.python.org/library/sets.html

01-18-2011, 06:30 AM	#4
Firebird Member Location: Germany Join Date: Jun 2010 Posts: 18	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

01-18-2011, 08:01 AM	#5
doc.ramses Member Location: Planet Earth Join Date: Jan 2011 Posts: 26	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.

01-19-2011, 01:16 AM	#6
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	You can also try Galaxy. I've found it very useful for set manipulation via a web browser.

01-19-2011, 07:57 AM	#7
Firebird Member Location: Germany Join Date: Jun 2010 Posts: 18	@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