I have analyzed a set of ChiP-seq data for a Transcription factor. I have my BigWig files and a list of genes names (ncRNA) I got from my overlap analyses. So I want to visualize the enrichment of my TF on these set of ncRNA genes. The tool I am using for generating the heatmap is deeptools2 (computeMatrix and plotHeatmap). So my question is how do I convert these list of ncRNA genes into an annotation file (BED format) using the UCSC Table Browser or any other tool?
Also, how can I get the complete annotation file for non-coding RNA KnownGenes (BED format) so I can visualize their enrichment around promoter site of my TF ChiP-seq data.
Can anyone kindly assist with useful information on how to go about this?