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Friday, September 20, 2013

Genomic Interval Tree, Interval manipulation

we do a lot of work on overlapping genomic features.
Bedtool is a great tool for this kind of task, but sometimes I want to implement it with python
for some custom usage. I found many useful links below. I have to digest them to fully understand how the  tree is constructed.

http://informatics.malariagen.net/2011/07/07/using-interval-trees-to-query-genome-annotations-by-position/

http://blog.nextgenetics.net/?e=45

http://hackmap.blogspot.com/2008/11/python-interval-tree.html

http://psaffrey.wordpress.com/2011/04/

http://www.biostars.org/p/2244/

I am by no means familiar with those algorithms.  Have a peek how other people do it, and learn from them is a good start for me.

Wow!

1 comment:

  1. see here:
    http://www.biostars.org/p/5785/
    http://www.biostars.org/p/53561/
    http://www.biostars.org/p/4126/
    http://bcbio.wordpress.com/2009/04/29/finding-and-displaying-short-reads-clustered-in-the-genome/

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