text: user1092: 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
  ...
  
  
  user294: 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 > bait1.txt
  cat bait1.txt | head -3
  chr1    831895  848168 
  chr1    831895  848168 
  chr1    831895  848168
  
  cat original.bed | cut -f 4,5,6 > 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. 
  
original_text: 1092: <p>Time for guess the bioinformatics file format... :)</p>
  
  <p>I found this '.bed' file on GEO (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84660" rel="nofollow noreferrer">GSE84660</a>), but it's clearly not a BED file. Anyone know what it <em>might</em> be? And what can view it? It's from a HiC expt.</p>
  
  <pre><code>#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
  ...
  </code></pre>
   294: <p>It looks like a weird way to represent data. You're right, it does not at all look like a <a href="http://genome.ucsc.edu/FAQ/FAQformat.html#format1" rel="nofollow noreferrer">BED</a>. </p>
  
  <p><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2247316" rel="nofollow noreferrer">Digging in GEO</a> made me find this information:</p>
  
  <blockquote>
    <p>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.</p>
  </blockquote>
  
  <p>So I think the authors merged a BED3 format plus additional BED-unrelated fields generating a tab-separated file - not clearly stated in their <a href="http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3935.html?foxtrotcallback=true#methods" rel="nofollow noreferrer">methods</a> though. The easiest would be to contact the authors maybe?</p>
  
  <p>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:</p>
  
  <pre><code>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
  </code></pre>
  
  <p>Not sure if it would fit your aims though. </p>
  
  <p>Also, for visualization of contact matrices, maybe you'll find <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1161-y" rel="nofollow noreferrer">this paper</a> useful. </p>
  