how to get total number of reads in a IGV view
Couldn't figure out how to get the total number of reads displayed in an IGV view... I somehow believe it should be available somewhere but I'm just missing it. Someone please let me know!!
Thanks~
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GenoMax
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changxu.fan
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changxu.fan
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move your mouse over the coverage histogram and wait for the contextual tooltip.
Your closest best is to try
igvtools count(LINK). You also need to keep in mind that IGV has a setting for downsampling reads (don't recall if that is set as default) so what you see in current view may not be all the reads in that interval.