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

[Matthew Speir]

Hello, Jie.

Thank you for your question about extracting data from a bigBed file.

The associated track description page contains details about the track data, including an explanation of what the numbers in the item names represent: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=encode4LongRnaTranscripts. You can click on the "Data schema/format description and download" to see a full description of the fields in this file.

A bigBed file can contain any number of extra fields beyond those in a standard BED file. For the file you are looking at, there are 8 extra fields, including one which contains a html table that will be displayed on the track description page.

To get a BED file contain just the standard fields, you can use the Unix cut command to strip the last 8 fields:

bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/mm10/encode4/encode4LongRnaTranscripts.bb stdout | cut -f1-12 > encode4LongRnaTranscripts.bed

If you want to strip the extra details from the item names, you could add a sed command with a regex pattern to remove this.

Even if you don't change the item names, once you've removed those extra fields, you should be able to run bedToGenePred and genePredToGtf to create a gtf file. 

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Genome Browser, User Support

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