Interpreting read coverage over gene body plot
Hi,
I'm working on some RNA-seq data for my thesis and I was hoping that someone could help me out.
My sequencing library was prepared using Illumina TruSeq Stranded mRNA kit and sequenced with a NovaSeq sequencer. After read alignment I did some post-aligment QC with RseQC and now I have this read coverage over gene body plot, which I am not sure how to interpret.
The curve starts at 0 in the 5' end of the gene body, but clips before it reaches 0 at the 3' end of the gene body.
Why is that? Does that mean that there is some sort of a bias? I looked up similar plots on the internet and the ones that have a bias are generally more slope-shaped.
Thanks!
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Is this a single end experiment? Could you post also a FastQC quality/position plot?
The data is paired-end and stranded with 100 bp reads. The per base Phred score is >35 for all of my samples across the whole read length.