I am looking for possible enhancer sequence and am looking at available Chip Seq data done by other researchers. The available data is posted on Facebase website, which is a website for craniofacial researchers (https://www.facebase.org/data/record/#1/isa:dataset/accession=FB00000860). This data is visualized in many BIGWIG tracks on to a genome browser with just chromosome positions and many bar graphs. I have never done Chip Seq myself and do not understand what these tracks mean. Also, can someone explain why the peaks appear at different positions in different tracks? Thank you.
2) The peaks must correspond to a protein binding the DNA at those spots, as detected by a given antibody. Maybe the peaks are at different spots due to different antibodies or different conditions.
The link is broken, but it doesn't matter for your question.
Any genome browser primarily displays the signal of a ChIP-Seq/RNA-Seq experiment ( and also all other -Seq experiments, variants, peaks, repeat-elements, etc etc etc etc).
For ChIP-Seq, what you see by a bar graph is the signal of a particular protein/histone activity at a given genomic location. If you are looking at a bargraph of a FOXA2 ChIP experiment, that means whenever there is a binding of FOXA2 at a genomic location, there will be bars (signals) and the height of bars represents the strength of FOXA2 protein (TF) binding. You need to understand what is the output of a ChIP-Seq experiment and what does it mean by a transcription-factor ChIP-Seq and Histone modification ChIP-Seq, which are two major readouts commonly used to define enhancers/promoters and to gain insights into genome cis-regulation.
So each track measures a different transcription factor or different histone modification signal, hence you see bars appearing at different places. Combinations of different assays are used to define enhancers/promoters etc
1) Link was broken for me
2) The peaks must correspond to a protein binding the DNA at those spots, as detected by a given antibody. Maybe the peaks are at different spots due to different antibodies or different conditions.
Need a picture or working link to help any more.