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 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
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