how should be coverage track of technical replicates of alignment visualization in BAM format?

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4.7 years ago

lkianmehr ▴ 100

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 BAM visualization • 758 views

ADD COMMENT • link 4.7 years ago by lkianmehr ▴ 100

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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 REPLY • link 4.7 years ago by ATpoint 81k

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How to add images to a Biostars post

ADD REPLY • link 4.7 years ago by WouterDeCoster 47k

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