Hello, [ Sorry for long question and description, but please read and help ]
We Did experiment in lab for 2 conditions : condition1 ( where TBP will not bind due to RNA interference ) condition2 (Where TBP probably bind to DNA TATA box ) We sequenced 2 condtions using illumina and got both Chip and Input (control) sequenced reads for each conditions like below : Chip data : 4 lanes reads ( I did concatenation using cat , to yield one read ) (it is a Single end not paired) Input or control data : 1 lane read ( its a paired end data ) I performed alignment to Human genome using Bowtie2 seperately for Chip and Input data , Then performed Peak calling by using Macs2 ( with default parameters ) : I got around 206 peaks and 1341 peaks for condition 1 and condition 2 respectively . But when i used bedgraph format of these peak file , to see in ensemble genome browser and when i restricted view to TBP gene , I couldn't find peaks at TBP neither ( saying No features detected) , nor TATA box Motifs by MEME analysis . Can anyone Expertee suggest me how can i interpret my results ? What should i considered Whether in both condition TBP didn't bind to DNA , So i didn't find the peak at TBP ? or Chipseq experiment failed ?