Question: bigWigAverageOverBed not accepting bed file
gravatar for Samuel
11 months ago by
Samuel10 wrote:

I'm trying to construct an IGV track that lets me visualise genome wide RNA expression level but i'm running into some problems trying to bin the data. This is what i did:

  • made a .bed file using bedtools makewindow with chrom.sizes as input
  • generated a bedgraph with bedtools genomecov
  • converted the bedgraph into bigwig with bedGraphToBigWig
  • tried to run bigWigAverageOverBed with the bed and bigwig file

then i got this error :

file genome250bp.bed doesn't appear to be in bed format. At least 4 fields required, got 3

which is rather strange, since the documentations for bed format only mentions the 1st 3 columns being required. Col 1 is my chromosome, col 2 and col 3 are are the start and end of each bin.

Thanks in advance

ADD COMMENTlink modified 11 months ago • written 11 months ago by Samuel10

BED has a minimum of 3 columns, which does not a tool can ask for more. $4 wold be a name field. Can be anything, like chr_start_end.

ADD REPLYlink written 11 months ago by ATpoint36k
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