I have sequenced human ChIP-Seq samples from 2 different experiments using Illumina. The number of reads are not equivalent between the 2 samples (Heart ChIP-Seq= 2million tags and Kidney ChIP-Seq= 10 million) and I have no replicates.
When ever I try to plot raw reads around promoters I'm failing (one flat line on top and another on bottom) because of the difference in number of reads. Does any one know what is the BEST way to deal this ?
I tried this [not successful ]
position_cDNAnorm = (position_cDNA / sum_cDNA) * average_sum_cDNA
- position_cDNAnorm = normalised cDNA value for specific position and specific DBP
- position_cDNA = cDNA value for specific position and specific DBP
- sum_cDNA = total cDNA count for specific DBP
- average_sum_cDNA = average of total cDNA counts of all DBPs DBP= DNA Bindign Protein (Transcription factor)