Can I use consensusSeeker for broad peak from macs2?

[xiasijian]

How can I import broad peak into R using consensusSeekeR?

[adeschen]

Hi Sijian Xia,

As the broad peak GRanges object has the same fields than the narrow peak GRanges, you should be able to use the broad peak Granges as input to the narrowPeaks parameter instead of a narrow peak GRanges. You will still need to add a specific row name information to the GRanges as described in the vignette. You will also need the corresponding peak parameter.

Best,
Astrid

[xiasijian]

Hi Astrid,
Thanks for your reply. The difference between narrow peaks and broad peak may be in the column"peak". In broad peak, the value in broad peak is negative. In your package, is negative value support? right?

[adeschen]

Hi Sijian Xia,

What is the definition of the peak column for a broad peak?

The peak definition for the narrowPeak format is the position of the summit relative to peak start. In presence of negative peak value, the summit would be located outside of the peak region. The consensusSeekeR package has not been developed/tested to support this case. However, it might still work out (with or without side effect).

A safer approach would be to relocate all peaks to the center of the regions.

Best,
Astrid