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arq5x / bedtools

A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
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Error using genomecov #129

Closed sengoku93 closed 6 years ago

sengoku93 commented 6 years ago

Hi,

I am running genomecov in order to take input bedfile and convert to bedgraph file. The plan is to use the converted bedgraph file so I can convert it to bigwig to plot a heatmap of ChipSeq data. However, when I try to use genomecov to get bedgraph:

bedtools genomecov -bg -i INPUT.bed -g hg19.genome

or bedtools genomecov -bg -i BCL6.bed -g hg19.chrom.sizes

I end up getting the same error: Input error: Chromosome chr17_random found in your input file but not in your genome file.

Any advice would be appreciated. Thank you!

arq5x commented 6 years ago

This is telling you that there are data entries for chr17_random in INPUT.bed or BCL6.bed but the length of that chromosome is not described in either hg19.genome or hg19.chrom.sizes. You will need to have all chromosome that are in your input (-i) represented in the genome (-g) file.