Question: how to explain expression level peaks(uneven gene expression) within a gene?
gravatar for Alexie Li
2.7 years ago by
Alexie Li20
Alexie Li20 wrote:

Hi all, I have a question about gene expression. I mapped RNA-seq reads back to the genome and noticed there are my expression peaks within a gene. Does it cause by library preparation process, sequencing problem, or a real biological thing? The blue bar on the top is a gene(single-exon gene), the red below is bam file generated by mapping reads. Has anyone got the same problem?

I uploaded the figure of a gene expression pattern on my GitHub, here is the link. Hope it works. I was thinking if there is a way to make uploading figure easier?

rna-seq expression assembly • 907 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Alexie Li20

What is the length of the exon ? Though it should not matter. Do you have a screen shot from IGV ? Did you filter for uniquely mapped reads ?

ADD REPLYlink written 2.7 years ago by geek_y10k

I think maybe I understand what is happening with the uneven expression. FastQC showed enriched clusters at the beginning of reads which means the library is biased by random priming during library preparation. Maybe it is why...

ADD REPLYlink written 2.6 years ago by Alexie Li20
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