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Old 08-23-2017, 01:19 AM   #1
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Default Finding the second next closest gene from a list of peaks


I am trying to find a way to find the second closest gene to a specific peak in a CHIP-seq.

There are many programs to find the closest gene, but I cannot seem to find away to get the second closest gene to a specific peak obtained from a CHIP-seq data.

Can anyone point me to a solution?
I am not very computer savy but I thought bedtools might be an option but I am not sure.

I am not interested in eliminating anything that overlaps the peak. I just want to see the two or more closest TSS to a given summit and distance. I also have a huge amount of peaks to process.

I am new here so sorry if I make any mistakes.

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