bigWigAverageOverBed not accepting bed file

Question

[Sam]

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

[ATpoint]

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.