Hello all,

This is my first time using MNASE data, and i am looking for a way to convert peaks to genes. From the peak file, I am a bit confused in selecting significant peaks or as what filter should be used to get the most significant peaks. The below file was generated from PuFFIN with columns peak (start and width), peak score, fuzziness, and curve level. What will this fuzziness term signify and how should a non-zero value of this should be interpreted?

head Rchr1.bed.nucs #(peaks for chromosome 1)

# Location      Peak_width      Score   STD(fuzziness)  Curve_level
28828.00        39.00   1.00    0.00    0.00
35567.00        33.00   1.00    0.00    0.00
41684.00        36.00   1.00    0.00    0.00
49437.00        29.00   1.00    0.00    0.00
49941.00        63.00   1.00    0.00    0.00
55062.00        38.00   1.00    0.00    0.00
55753.00        74.00   1.00    0.00    0.00
56157.00        52.00   2.00    6.75    0.00
68266.00        92.00   2.00    18.00   0.00

I would also appreciate if someone can point me to commonly used pipeline for MNASE ChIP-Seq data.

Thanks.