Intersect between bedGraph and bed file

Question

[daffodil]

Hi , I have sorted BAM files and would like to generate a bedGraph file that includes normalized counts of reads. I used Bedtools for this purpose. Then, I wanted to extract read counts based on a BED file of TSS regions. However, the intervals in the bedGraph file differ from the intervals in the TSS file. I used the -d option in Bedtools to measure the counts at each position and then intersect between bedGraph and bed file. Is this approach correct? bedtools genomecov -ibam "${sorted_bam}" -d -scale "${scale_factor}" > "${output_dir}/${sample}.scaled_combined_strands.bedGraph"