more doc

chipseq_workflow/cs_snippets.sh

@@ -129,3 +129,15 @@ mailme "phantom qc done"
 
 ## differential binding diffbind
 
+
+diffReps
+"Negative Binomial tests implemented in diffReps (Shen et al. 2013) were used to detect differential histone
+modification regions using a sliding window of 600bp (H3K4me3) or 5000bp (H3K27me3), p-value cutoff 1e-
+6, sharp peaks mode for H3K4me3 (--nsb 20) and broad peak mode for H3K27me3 (--nsb 2), hg19 as reference
+genome, and an average fragment size of 250bp (rest of parameters default). Differential histone modifications
+regions not overlapping (at least 1bp) significant chromatin marks previously detected during peak calling at
+least in one of conditions under comparison were removed. Regions were ranked by their fold-change (FC), and
+reported as differentially enriched only if the absolute FC≥1.5, and Benjamini-Hochberg corrected p-value≤1e-3.
+As described on the figures, figure legends and results, for Fig. S6C and S6D only the thresholds for
+statistical significance were relaxed as it follows: binomial test p-value cutoff 1e-4 (diffReps standard); absolute
+FC≥1.25, and Benjamini-Hochberg corrected p-value≤1e-2 (FDR 1%)."