Question: how should be coverage track of technical replicates of alignment visualization in BAM format?
0
gravatar for lkianmehr
11 months ago by
lkianmehr50
France
lkianmehr50 wrote:

Hello,

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
1

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.

ADD REPLYlink written 11 months ago by ATpoint36k

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ADD REPLYlink written 11 months ago by WouterDeCoster44k
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