weird behaviour on bedtools

Question

[barrypraveen]

Hi All,

I want to extract the counts on defined regions (my.bed). But i'm not able to understand the results. The command says extract the counts form the bam files using bed file also the region of the bed region has to have >=80%.

multiBamCov -f 0.80 -bams  1.bam 2.bam  -bed my.bed > output.bed

sample result.

14  21853003    21853010    1   2   ENST00000390435 5   5

According to the multiBamCov i have 5 reads the regions i defined but the IGV shows different count.

Why is that?

[MatthewP]

Maybe IGV not displaying all reads? (downsample display).