Annotate counts region by region

Question

[elb]

Hi guys, I know it could be an answer 1000 times redundant but I looked around without find a quick solution. I have 5 .bam files and a .gtf file that looks like this:

     1    134202951   134202953
     1    134202954   134203590
     1    134199215   134203590
  

where 1 indicates chromosome 1 and the other two columns respectively start and end position of the chromosome region. I simply would like, for each start-end to have the number of counts. I tried using

  overlap.counts1 <- countOverlaps(bedfile,bamfile1)
  

for a single file but it outputs the total number of counts not region per region. Can anyone help me please?

thank you in advance

[h.mon]

There are several similar threads, maybe one of them has a suitable solution.

Counting Number Of Bam Reads Directly Within Set Of Intervals With Bedtools

How To Calculate The Coverage Of A Specific Interval Based On Data From A Bam File

how to get the coverage for the entire interval

Read depth interval comparison

Also see this function: calculateBamCoverageByInterval().