Hey Daniel, I think that it would be better to use same options that the original paper used.
From the supplementary information:
"The identification of ChIP-seq enriched regions (peaks) in each sample was performed using
HOMER (http://homer.salk.edu/homer/). For histone modifications, peaks were identified by
searching locations of high read density using a 1000 bp sliding window. We required adjacent
peaks to be at least 1000 bp away to avoid redundant detection. The threshold for the number of
tags that determined a valid peak was selected at a false discovery rate of 0.001. The following
HOMER command was used:
cmd = findPeaks -L 0 -C 3 -size 1000 -
minDist 1000 -tbp 3 -o
danobaji
commented
4 years ago
Hey Daniel, I think that it would be better to use same options that the original paper used.
From the supplementary information:
"The identification of ChIP-seq enriched regions (peaks) in each sample was performed using HOMER (http://homer.salk.edu/homer/). For histone modifications, peaks were identified by searching locations of high read density using a 1000 bp sliding window. We required adjacent peaks to be at least 1000 bp away to avoid redundant detection. The threshold for the number of tags that determined a valid peak was selected at a false discovery rate of 0.001. The following HOMER command was used: cmd = findPeaks -L 0 -C 3 -size 1000 -
minDist 1000 -tbp 3 -o