Details
-
Type:
Support
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Labels:None
Description
The Biostars post can be found here:
https://www.biostars.org/p/139264/
User paedugar wrote Question: Can IGB load BED 6+3 files?:
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.
Attachments
Issue Links
- relates to
-
IGBF-593 Add support for the broadPeak and narrowPeak formats
-
- Closed
-
Activity
User pgarcia commented:
That sounds easy I'll try it out. Thanks!
User Ann wrote Answer: Can IGB load BED 6+3 files?:
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
User Nowlan Freese wrote Answer: Can IGB load BED 6+3 files?:
Hi pgarcia,
The .broadPeak format is not a currently supported file format in IGB, hover 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