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  • How to give peaks data of ChIP-seq annotation

    Hi everyone

    I want to ask you how to give peaks data of ChIP-seq annotation.
    For understanding peaks data generated by MACS as bed file or xls file of peaks, I want to know What genes including each peak or Which peaks were included in intergene.
    However I'm beginner of bioinformatic analysis and don't have a teacher of bioinformatician in my lab.

    What software should I use? or What should I learn?
    Sorry that I don't have knowledge enough...
    For analysis, I use linux

    Thanks in advance

  • #2
    I guess you have an annotations file... so you can easily have a bed file with the gene coordinates.

    You can either use intersectBed from bedtools (option -v to have non overlapping regions).

    Or with R and the package Rsamtools, you can use the functions setdiff, intersect, findOverlaps... (just keeping in mind you want first to have a GRanges object of your intergnic regions first, which you will have to make).

    s.

    Comment


    • #3
      Thank you for answer.
      Sorry that I have not studied enough.

      On the basis of your hint, I will study more

      Comment

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