running MACS for Drosophila

This is how to run MACS for ChIP-seq data analysis.


effective genome size is for Drosophila melanogaster and pvalue is chosen.


macs -t 100014_modENCODE_CTCF_IP_s_1_filtered_eland_result.txt -c 100014_modENCODE_CTCF_Input_s_2_filtered_eland_result.txt --format=ELAND --gsize=120000000 --tsize=36 --pvalue=1e-3 --bw=250 --mfold=7 --name=CTCF_mf7_100014_14 --wig --diag

Use plotrix package to generate nice image of matrix.

Here is how I use color2D.plot function from library (plotrix)


color2D.matplot (idt, redrange=c(0,1), greenrange=c(0,0), bluerange=c(0,0), xlab = "presence", ylab ="insulator combination")