Question: how should be coverage track of technical replicates of alignment visualization in BAM format?
gravatar for lkianmehr
11 months ago by
lkianmehr50 wrote:


short read sequence alignment of RNA-seq in Bam format are visulaized using IGV, something is wrong I think, technical replicates of each sample are not exactly same, I mean coverage track of them is not identical even with same data range. Do you know it should be same? or is it normal?

thanks in advance

igv visualization bam • 281 views
ADD COMMENTlink written 11 months ago by lkianmehr50

If you load BAM files they are basically never the same which is normal and expected as read counts between files are never 100% the same. If one BAM has 20% fewer reads it gets 20% reduced signal given the samples were truely identical. Please search the web towards the topic normalization.

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