I have been testing WIGs made from the same ChIP-Seq bam file but using two different tools with two different results:
1) Macs with -w -S --space=50 --keep-dup=1
2) igvtools count with -e 160 -w 50
The cell type I'm interrogating has a well-known focal amplification event of about 1 megabase. In this region, the Macs WIG has a plateau of signal across the whole region but the igvtools WIG has distinct peak signals with a slight increase in background noise. Is there a known reason these should differ so drastically, despite using 1 read per position in Macs?
•
written
by
snarkyscientist •
MACS removes the duplicated reads when make wig file?
Yep. Chalk this up to my inexperience with igvtools. I somehow thought that "count" was removing duplicates.
•
written
by
snarkyscientist •
MACS removes the duplicated reads when make wig file?
Log in to answer this question.
