Hi, everyone

I want to know the count of reads that overlap, this is the bed file, when I used IGV I found that in position for example, 51693268-51693291 of microRNA-125 on differents bams file have 12, 73, 75, 379, 400

chr19    10552122    10552144    hsa-miR-1238-5p
chr19    51693268    51693291    hsa-miR-125a-5p
chr19    20399320    20399342    hsa-miR-1270
chr19    13874910    13874932    hsa-miR-181d-5p
chr19    10817469    10817491    hsa-miR-199a-5p
chr19    28798188    28798210    hsa-miR-3134
chr19    813590    813612    hsa-miR-3187-5p
chr19    18282129    18282151    hsa-miR-3188
chr19    18386570    18386594    hsa-miR-3189-5p
chr19    47226988    47227010    hsa-miR-3190-3p
chr19    47226952    47226974    hsa-miR-3191-3p
chr19    45639009    45639031    hsa-miR-330-3p
chr19    4770700    4770723    hsa-miR-3529-3p
chr19    53787716    53787738    hsa-miR-371a-3p
chr19    53787678    53787700    hsa-miR-371b-3p
chr19    53787931    53787953    hsa-miR-372-3p
chr19    53787895    53787917    hsa-miR-372-5p
chr19    53788748    53788770    hsa-miR-373-3p
chr19    20027075    20027100    hsa-miR-3916

When I used multicov from bedtools

bedtools multicov \
  -bams SRR1054203.segemehl_chr19.sam.bam.sorted.bam \
  SRR1054204.segemehl_chr19.sam.bam.sorted.bam \
  SRR1054205.segemehl_chr19.sam.bam.sorted.bam \
  SRR1054206.segemehl_chr19.sam.bam.sorted.bam \
  SRR1054207.segemehl_chr19.sam.bam.sorted.bam \
  SRR1054208.segemehl_chr19.sam.bam.sorted.bam \
  -bed ../genome/chromosome.19_hsa_mature.fasta.bed.out > conteo_mature_hsa_microRNAs

chr19    10552122    10552144    hsa-miR-1238-5p    0    0    0    0    0    0
chr19    51693268    51693291    hsa-miR-125a-5p    0    0    0    0    0    0
chr19    20399320    20399342    hsa-miR-1270    0    0    0    0    0    0
chr19    13874910    13874932    hsa-miR-181d-5p    0    0    0    0    0    0
chr19    10817469    10817491    hsa-miR-199a-5p    0    0    0    0    0    0
chr19    28798188    28798210    hsa-miR-3134    0    0    0    0    0    0
chr19    813590    813612    hsa-miR-3187-5p    0    0    0    0    0    0
chr19    18282129    18282151    hsa-miR-3188    0    0    0    0    0    0
chr19    18386570    18386594    hsa-miR-3189-5p    0    0    0    0    0    0
chr19    47226988    47227010    hsa-miR-3190-3p    0    0    0    0    0    0
chr19    47226952    47226974    hsa-miR-3191-3p    0    0    0    0    0    0
chr19    45639009    45639031    hsa-miR-330-3p    0    0    0    0    0    0
chr19    4770700    4770723    hsa-miR-3529-3p    0    0    0    0    0    0
chr19    53787716    53787738    hsa-miR-371a-3p    0    0    0    0    0    0
chr19    53787678    53787700    hsa-miR-371b-3p    0    0    0    0    0    0
chr19    53787931    53787953    hsa-miR-372-3p    0    0    0    0    0    0
chr19    53787895    53787917    hsa-miR-372-5p    0    0    0    0    0    0
chr19    53788748    53788770    hsa-miR-373-3p    0    0    0    0    0    0
chr19    20027075    20027100    hsa-miR-3916    0    0    0    0    0    0
chr19    804977    804999    hsa-miR-4745-3p    0    0    0    0    0    0
chr19    804941    804963    hsa-miR-4745-5p    0    0    0    0    0    0
chr19    4445987    4446009    hsa-miR-4746-5p    0    0    0    0    0    0
chr19    49933073    49933096    hsa-miR-4751    0    0    0    0    0    0
chr19    58386827    58386849    hsa-miR-4754    0    0    0    0    0    0

What could be the problem? Thank you for your time and consideration

Cordially,
Adriana