in reply to how to get clusters?

The answer depends on your definitions of cluster, hits and bp.

Like eric256, I don't believe I understand your question.

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Re^2: how to get clusters?
by sirna (Initiate) on Jan 04, 2008 at 15:33 UTC
    hi, the hits are the matches of smallRNAs against the genome(have their coordinates like start and stop in a file example: 105, 1) . the clusters are grouping of these hits into one big cluster if only the other cluster is 200 basepairs away from the initial hit. as i have mentioned inthe previous post, the first three should be made into one cluster ie the cordinates of the first cluster would be 1 , 105.
[reply]

      You still haven't provided enough context free of jargon from your problem domain to let people clearly answer your question. Reading I know what I mean. Why don't you? and How (Not) To Ask A Question would probably be helpful at this point. Don't make people drag everything out of you tooth and nail in order to give you help.

      Update: Not to mention given the apparent problem domain if this is a common file format it's likely BioPerl has an off the shelf module to do this already . . .

      The cake is a lie.
      The cake is a lie.
      The cake is a lie.

[reply]
      You're still making a lot of assumptions. Is 105,1 == 1,105? How do you determine the distance in basepairs between clusters? How is a cluster represented when it is displayed?

      I suspect that if you could explain how to solve the problem you'd be able to write the program yourself.

[reply]

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