I would like to extract intron-exon reads (unspliced reads) from bam file. I tried use the with following command command, bedtools intersect -s -F 1 -split -a input.bam -b junction.bed >Intron_out.bam
Where junction.bed consists of last bp intron and first bp exonic. It doesn't to seem to be working, because, I am also getting the split reads that I am not expecting.
I would really appreciate, if someone can help me with the same.