genomic reads count

Question

[13263617869xf]

Hi everyone,i want to count exon、intron、intergenic、exon-exon、exon-intron reads,now i konw how to use the bedtools like tools to solve tie problem,but i think my solution will have overlap count with them(need to prepare bed file form GTF file),so has anyone have new solution or a tools or packages to deal this problem,thanks!

[Sej Modha]

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What have you tried so far? Do you have a .sam or a .bam file or raw sequencing reads in .fastq format?