Hello everyone!

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?
<p>Since you have a NarrowPeak file of ChIP signal peaks, and you have aligned ChIP signal, you can use either file (with slight differences) to measure whether one feature (exon, intron, exon-intron boundaries, intron-exon boundaries, 5&#39; vs 3&#39; exons) tends to have a greater signal (normalized to feature length). Bedtools should be able to do this, once you&#39;ve constructed your different feature files in BED format (or similar), and I&#39;m sure there are more sophisticated solutions.</p>
