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  • Finding the second next closest gene from a list of peaks

    Hello,

    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.

    Thanks.

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