I am thinking of mapping reads onto gene bodies to make it less strict for off-target identification. Wondering if there's any file there already, or I have to extract certain regions manually. Thanks!
I would get the fasta file of the human transcripts and map it against it. You can get the RefSeq annotation from here.
Then you can build an index with your favorite aligner and align against it.
Other option would be to extract the genes from a gtf annotation and use bedtools getfasta to get the fasta file from the desired intervals.