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.

For more information about bed format: https://genome.ucsc.edu/FAQ/FAQformat.html#format1

For more information about broad peak format: http://genome.ucsc.edu/FAQ/FAQformat.html#format12

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

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