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bedGraphToBigWig error in README example

Open jmschrei opened this issue 4 years ago • 3 comments

Howdy

I was working through the example, and when I got to the following code snippet

# get coverage of 5’ positions of the plus strand
bedtools genomecov -5 -bg -strand + \
        -g hg38.chrom.sizes -ibam merged.bam \
        | sort -k1,1 -k2,2n > plus.bedGraph

# get coverage of 5’ positions of the minus strand
bedtools genomecov -5 -bg -strand - \
        -g hg38.chrom.sizes -ibam merged.bam \
        | sort -k1,1 -k2,2n > minus.bedGraph

# Convert bedGraph files to bigWig files
bedGraphToBigWig plus.bedGraph hg38.chrom.sizes plus.bw
bedGraphToBigWig minus.bedGraph hg38.chrom.sizes minus.bw

I encountered the following error when running bedGraphToBigWig using hg38.chrom.sizes from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes:

chrEBV is not found in chromosome sizes file

jmschrei avatar Sep 23 '20 22:09 jmschrei