I'm relatively new to Bioinformatics so please bare with me. A Ph.D student in my lab has asked me to analyze ChIP-Seq data and determine whether peaks fall into exons, introns, or exon-intron junction categories. The gene she is looking at is TNFAIP3 and the mark she wants me to analyze is Pol II. I am using the hg19 human model.
Unsure how to start I am thinking of doing the following:
1) Download BED files for TNFAIP3 and get individual files for Exons, and Introns.
2) Annotate peaks of BED files using a python script already written using Homer.
After this I am unsure how to continue. Am I done once I have these annotations in a txt format that can be opened on excel? Her second question revolves around analyzing peaks for common sequence motifs so how would I prepare this information to continue into that?