Interpreting read coverage over gene body plot

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2.7 years ago

Mikael • 0

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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chipster rseqc illumina rna-seq • 1.1k views

ADD COMMENT • link 2.7 years ago by Mikael • 0

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Is this a single end experiment? Could you post also a FastQC quality/position plot?

ADD REPLY • link 2.7 years ago by Shred ★ 1.4k

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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.

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ADD REPLY • link 2.7 years ago by Mikael • 0

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