Question: Can IGB load BED 6+3 files?
2
gravatar for pgarcia
5.0 years ago by
pgarcia20
United States
pgarcia20 wrote:

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 • 1.7k views
ADD COMMENTlink modified 5.0 years ago by Ann2.3k • written 5.0 years ago by pgarcia20
2
gravatar for Nowlan Freese
5.0 years ago by
Nowlan Freese850
United States
Nowlan Freese850 wrote:

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

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Nowlan Freese850

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

ADD REPLYlink written 5.0 years ago by pgarcia20
2
gravatar for Ann
5.0 years ago by
Ann2.3k
Concord NC USA
Ann2.3k wrote:

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

ADD COMMENTlink written 5.0 years ago by Ann2.3k
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