What format is this? Pretty sure it's not a BED file Time for guess the bioinformatics file format... :)

I found this '.bed' file on GEO (GSE84660), but it's clearly not a BED file. Anyone know what it might be? And what can view it? It's from a HiC expt.

#column headers: bait1_chr, bait1_start, bait1_end, bait2_chr, bait2_start, bait2_end, contact_ID, NA, NA, B1_D0_counts, B1_D3_counts, B1_D6_counts, B2_D0_counts, B2_D3_counts, B2_D6_counts

chr1    831895  848168  chr1    850619  874081  b2b_1   .       .       114     125     127     75      97      92
chr1    831895  848168  chr1    889424  903640  b2b_2   .       .       15      12      16      4       15      20
chr1    831895  848168  chr1    903641  927394  b2b_3   .       .       13      13      10      18      15      8
...
It looks like a weird way to represent data. You're right, it does not at all look like a BED. 

Digging in GEO made me find this information:


  Supplementary_files_format_and_content: Tab-delimited file reports one
  contact per row. Interacting HindIII fragments are represented in bed
  format (chr/start/stop) with bait (or upstream bait, in the case of
  b2b contacts) listed first. The following fields correspond to a
  unique contact ID, fragment IDs for first and second fragments, and
  raw read counts supporting contacts in each replicates.


So I think the authors merged a BED3 format plus additional BED-unrelated fields generating a tab-separated file - not clearly stated in their methods though. The easiest would be to contact the authors maybe?

Depending on your aims, if you only need the first 3 fields (but I doubt it) I would reformat this "bed" file (to make it processable as a BED file) in two sub-files:

cat original.bed | cut -f 1,2,3 &gt; bait1.txt
cat bait1.txt | head -3
chr1    831895  848168 
chr1    831895  848168 
chr1    831895  848168

cat original.bed | cut -f 4,5,6 &gt; bait2.txt
cat bait2.txt | head -3
chr1    850619  874081  
chr1    889424  903640
chr1    903641  927394


Not sure if it would fit your aims though. 

Also, for visualization of contact matrices, maybe you'll find this paper useful.