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igv and bam file

Hi all,

I have a quick and probably easy question. I am new to igv and I want to find the number of alignments in the bam file which aligned to genome. (To be clear I am trying to find number of alignments in the red box which indicated in the image)

Thanks in advance :)

enter image description here

igv rna-seq bam
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updated by Ram Ram • written by biology_inform • biology_inform

Have you tried bedtools?

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written by swbarnes2 swbarnes2

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