Getting peak (bed narrowPeak) from signals (Wig)

Question

[arsala521]

Hi,

I have a wig file for TF ChIP-seq experiment. I am copying few of its lines:

X 3305 3340 7.62538579029898
X 3405 3440 6.14333110000589
X 3505 3540 4.47699219685019
X 3605 3640 2.80930393197141

From this wig file, I need bed narrowPeak file.

Should I first convert it to bedGraph and then use MACS subcommand bdgpeakcall, or should I use bedops utility wig2bed.

I have always retrieved TF ChIP-seq data in bed narrowPeak format. This is my first time working with Wig. Would be very grateful for any help.

Answer 1

[Alex Reynolds]

The wig2bed tool will just convert Wig over to (in your case) five-column BED, whereas you definitely want to do some kind of peak calling. You want to get narrowPeak-formatted BED, where there is somewhat more metadata (including strand and peak offset). I don't know what the score values in your Wig files represent, so I couldn't say if MACS2 would be appropriate -- but probably something in that direction makes sense.

[arsala521]

Got it. Thanks.