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  • Empty bedGraph file (from bed file)

    Hi there,

    I am trying to convert my bed file to bedGraph. I've done the conversions using three different types of methods like at below;

    1. bedtools genomecov -i forebrain.bed -g mm10.chromsizes.tab -bg > forebrain.bedgraph
    2. bedItemOverlapCount $index -chromSize=mm10.chromsizes.tab forebrain.bed+ | sort -k1,1 -k2,2n > forebrain.bedgraph
    3. awk '{printf "%s\t%d\t%d\t%2.3f\n" , $1,$2,$3,$5}'' forebrain.bed > forebrain.bedgraph

    Three of the methods generate .bedgraph files, but the files from #1 and #2 methods are empty and the file from #3 only has one line. My .bed file contains selected 1470 peaks from ChIP-Seq and I wanted to upload them to UCSC genome browser with their score (bedgraph or bigwig). For the reference, I attached the format of my .bed file at below;

    chr2 98667062 98667179 chr2-1 62083.2 +
    chr2 98662802 98662919 chr2-2 42337.9 +
    chr2 98662210 98662327 chr2-3 33591.3 +
    chr9 35305400 35305517 chr9-1 20550.2 +
    chr14 19415778 19415895 chr14-1 12999.2 +

    I tried to manually organize the bed format to bedgraph (I was not sure it was correct) using excel sheet like at below;

    chr2 98667062 98667179 62083.2
    chr2 98662802 98662919 42337.9
    chr2 98662210 98662327 33591.3
    chr9 35305400 35305517 20550.2
    chr14 19415778 19415895 12999.2

    But, I got an error (Error Unrecognized format type=bedGraph line 2 of https://dl.dropboxusercontent.com/u/...9/forebrain.bg) when I uploaded them to UCSC browser. I can't figure out what I was wrong. Could you help me if you know this type of issue? Thank you.

    Thank you.

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