Wig file obtained from MACS14 is longer than chromosome size?

Question

[secretloong]

The wig file:

variableStep chrom=chr15 span=1
...
12968274        1

But my chromosome size is chr15 12968165. Wig file is longer than chromosome?

The parameters:

./MACS14 -t ...bed -c ...bed -s 49 -g 1.1e+9 -p 1e-5 --nomodel -w -S --space 1 -m 10,30

Could someone give me a hand?

Answer 1

[dfornika]

I've run into the same problem. I can't explain why MACS produces wig files like this, but I have a quick fix. I used bedClip to trim off the ends of the wig files.

There is a nice brief blog post written by Sukhdeep Singh on how to use bedClip here.

Answer 2

[Ming Tommy Tang]

Yes, MACS extend the reads to 300bp, so it will exceed the limits of the chromosome. bedgraph files generated from it also has the same problem. If you upload to UCSC, it will complain errors. As suggested, use bedClip first