I have bam files of 8 samples (4 normal and 4 diseased), produced by alignment with novoalign (small-rna sequencing data). I have excluded the mirna from the bam files by using the following command:
bedtools intersect -v "sample.bam" "hg19_mirna.gff3" > output.bam
In this manner I have excluded the miRNA from all the samples. Now I want to find the utr (3' and 5') sequences present in the resultant bam files, and the read counts of each of the utr sequences.
Could anyone suggest a way to do this?