mapping status for each region

Question

[a.hasankhani74]

Hi. I have bam file from hisat2 aligner in RNA-seq data analysis.I used from samtools flagstat for mapping status but I want percentage of reads mapped to each region separately.

how to generate The percentage of reads mapped to exonic, intronic and intergenic regions.

Answer 1

[ATpoint]

Please use the search function:

Percentage of RNA-seq reads in exonic, intronic, intergenic and splice junction regions

Easiest way to compute RNA-Seq mapping stats (exons, introns, intergenic)?

Number of aligned reads in exon, intron ...