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bedGraphToBigWig error in README example
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