Question: find overlap of bed files of different length
8.8 years ago by
Duke • 210
Duke • 210 wrote:
On 1/31/11 1:20 PM, Kasper Daniel Hansen wrote: > Use findOverlaps to find all cases. This is usually the hard and big > computation. Then use for example pintersect() to compute the actual > overlap in percent. There might be some tedious coding involved. Thanks for your suggestion Kasper, though honestly I have not tried it yet. But based on what Martin and you suggested, I thought the final code will not run fast because of extracting to strand/subset and running each. Especially my task is a little more complicated: I need to find gene expressions (counting sequences in exonic regions of each gene). I also gave BEDTools a try, but it does not fulfil my needs (extremely slow for a gene list of 28k). I ended up with coding a c++ code to do the job. Thanks for all of your suggestions and helps guys. D.
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