I have a list of 10 genes that i want to find level of enrichment in a public data set. So I downloaded FAStq files and run the alignment with Bowtie, Macs for peaks. Now my question is how should i Specifically check the status of these selected 10 genes in analyzed data. I can take an indirect approach that annotate MACS peaks first and see overlap of the selected genes. I was wondering is there any direct approach of sub-setting Peaks data corresponding to my 10 selected genes. I only have gene ids- hugo gene names.
Thanks for the input.