Question about bigbedtobed output

[Jie Song]

Hello!

I'm converting .bb file to .bed with bigBedToBed tools, but got weird content in bed file, like this:

  chr1 3206472 3215682 ENSMUSG00000051951[2,2,3] 0 - 3215682 3215682 0,0,0 2 845,2244, 0,6966, HAVANA ENSMUSG00000051951.5 Xkr4 ENSMUSG00000051951[2,2,3] Xkr4[2,2,3] 1.09 Max score(s) in <br>hippocampus_14d: 1.06<br>hippocampus_2mo: 1.09 <table> <tr><td>adrenal_10d</td><td>0.0</td></tr> <tr><td>adrenal_14d</td><td>0.0</td></tr> <tr><td>adrenal_18-20mo</td><td>0.0</td></tr> <tr><td>adrenal_25d</td><td>0.0</td></tr> <tr><td>adrenal_2mo</td><td>0.0</td></tr> <tr><td>adrenal_36d</td><td>0.0</td></tr> <tr><td>adrenal_4d</td><td>0.0</td></tr> <tr><td>adrenal_gland</td><td>0.39</td></tr> <tr><td>c2c12_myoblast (cell line)</td><td>0.0</td></tr> <tr><td>c2c12_myotube (cell line)</td><td>0.0</td></tr> <tr><td>cortex</td><td>0.05</td></tr> <tr><td>cortex_14d</td><td>0.0</td></tr> <tr><td>cortex_18-20mo</td><td>0.62</td></tr> <tr><td>cortex_2mo</td><td>0.66</td></tr> <tr><td>f1219 (cell line)</td><td>0.0</td></tr> <tr><td>forelimb_e11</td><td>0.0</td></tr> <tr><td>forelimb_e13</td><td>0.0</td></tr> <tr><td>gastroc_10d</td><td>0.0</td></tr> <tr><td>gastroc_14d</td><td>0.0</td></tr> <tr><td>gastroc_18-20mo</td><td>0.0</td></tr> <tr><td>gastroc_25d</td><td>0.0</td></tr> <tr><td>gastroc_2mo</td><td>0.0</td></tr> <tr><td>gastroc_36d</td><td>0.0</td></tr> <tr><td>gastroc_4d</td><td>0.0</td></tr> <tr><td>heart_14d</td><td>0.0</td></tr> <tr><td>heart_18-20mo</td><td>0.0</td></tr> <tr><td>heart_2mo</td><td>0.0</td></tr> <tr><td>hippocampus</td><td>0.44</td></tr> <tr><td>hippocampus_10d</td><td>0.0</td></tr> <tr><td>hippocampus_14d</td><td>1.06</td></tr> <tr><td>hippocampus_18-20mo</td><td>0.33</td></tr> <tr><td>hippocampus_2mo</td><td>1.09</td></tr></table>

  

The gene_id is ENSMUSG00000051951[2,2,3] instead of ENSMUSG00000051951, and there are some html content in the end. The original bb file is https://hgdownload.soe.ucsc.edu/gbdb/mm10/encode4/encode4LongRnaTranscripts.bb

What should I do to get a clean bed?

Thanks for your time. Looking forward for your reply.

Jie Song