specifying chromosome sizes and output with bedGraphToBigWig
I have a bedgraph of a full genome mm9:
chr1 3049360 3053345 0
chr1 3049360 3053345 0
chr1 3049360 3053345 0
chr1 3049360 3053345 0
chr1 3049360 3053345 0
I want to convert it to a bigwig:
bedGraphToBigWig HET.bedgraph mm9_genome HET.bw
Where the mm9_genome specifies the chromosome sizes.
However I keep getting this error
invalid unsigned integer: "size"
mm9_genome file is as follows:
chr1 197195432
chr2 181748087
chr3 159599783
chr4 155630120
chr5 152537259
chr6 149517037
chr7 152524553
chr8 131738871
chr9 124076172
etc.
Can anyone help?
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The error sounds like there is a string somewhere in your files (bedgraph or genome file) where there is supposed to be a integer. Try grepping for "size" in either files.
Your example bedGraph file has the same region repeated. You can't have overlapping regions in bigWig files.