Can IGB load BED 6+3 files?
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7.2 years ago
pgarcia ▴ 20

Is it possible to load the "broad peak" output files of macs2 (BED 6+3) into the Integrated Genome Browser (IGB)?

I have tried with no luck, I'm not quite sure whether I need to specify the input format.

igb macs2 • 2.4k views
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7.2 years ago
Nowlan Freese ▴ 860

Hi pgarcia,

The .broadPeak format is not a currently supported file format in IGB, however it can easily be converted to the more common .bed format, which is supported.

To convert the file to a bed file, limit the data to the first 6 columns. To do this on the command line use:

\$cut -f1-6 FILE.narrowPeak > NEWFILE.bed


Optionally, you can replace the score field (column 5) with any one of the latter fields (columns 7-9 from broad peak format) to make that value appear as the score.

These file formats (both broadPeak and narrowPeak) have been recently requested by users, and we are preparing to add support for them in the near future.

Nowlan

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That sounds easy I'll try it out. Thanks!

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7.2 years ago
Ann ★ 2.3k

We have a pending request to support these two formats without the need for manipulating files, and so now probably would be a good time to move ahead with implementing this. When it's ready, we'll post back here to let you know.

Regards,

Ann