Before I used MEME to search the upstream of genes aiming to look for any motifs. Now, I'm using motifs from MEME and use FIMO to scan through the genome to find whether there are other locations of these motifs.
I got a tsv file from the FIMO, which contains
motif_id | motif_alt_id | sequence_name | star | stop | strand | score | p-value | q-value | matched_sequence
I was wondering if there is any method to compare the motif location with the location of the features?
For example, I expect to see their occurrence in the intergenic region/ partially overlap with gene/ totally within the gene.
Thank you in advance