why different read coverage in the same gene in one sample

[sadiexiaoyu]

Hi, All,

I am using IGV to view my bam result. And I am confused why there are different read coverage in the same gene. I mean, ideally, the read coverage should be even across the gene. But in some cases (for example, see the two attachments), I found the read coverage is significant difference across gene. Could anyone help explain this? Thanks!

Best,

Sadiexiaoyu

[dpryan]

This is normal. Firstly, "random hexamer priming" is actually not that random. That leads to a lot of the waviness that you see. Secondly, there are also 5' to 3' biases, caused be the library construction step and RNA degradation. There are also mapability differences across the length of a gene (which can interact with the SNPs that are present in samples).

[sadiexiaoyu]

This is normal. Firstly, "random hexamer priming" is actually not that random. That leads to a lot of the waviness that you see. Secondly, there are also 5' to 3' biases, caused be the library construction step and RNA degradation. There are also mapability differences across the length of a gene (which can interact with the SNPs that are present in samples).

Hi, dpryan,

Thanks!

Best,

Sadiexiaoyu