23 months ago by
CRUK, Cambridge, UK
The peak caller name
MACS2 is not recognized, it defaults to
raw, which looks for the peak score in the fourth column (chromosome, start, end, score). I'm not sure what the format of your Peaks files. If it is really BED format, it should have five columns: chromosome, start, end, name, score (score in the fifth column). In this case, you can enter
bed instead of
MACS2 in the
PeakCaller column. Alternatively, you can add another column,
ScoreCol, and include the column number with the scores (5).
Another option is to use the .
xls files from MACS2 instead of the
bed files, and set the
If you're still having a problem, post the first two or three lines from one of the peak files here and I'll help sort it out.