Question: Association between number of exons and read density
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gravatar for lkmklsmn
4.6 years ago by
lkmklsmn870
United States
lkmklsmn870 wrote:

Hi,  

I am analyzing human cell line RNAseq data. I have generated gene level read densities by dividing total read counts by gene length.  

Now I have an extremely strong correlation (P<1e-100) between this read density and the number of exons contained in a gene. Something seems wrong here. Is this normal? Any ideas where or how I could have messed up the normalization? Has anybody recognized this relationship before?

 

ADD COMMENTlink modified 4.6 years ago by mikhail.shugay3.3k • written 4.6 years ago by lkmklsmn870
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gravatar for mikhail.shugay
4.6 years ago by
mikhail.shugay3.3k
Czech Republic, Brno, CEITEC
mikhail.shugay3.3k wrote:

Hello! RNA-Seq should normally contain a relatively small fraction of intronic reads. On the other hand introns are far longer then exons, so it is the major factor that determines gene length. So one should normalize by CDS length, not the total length of gene.

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by mikhail.shugay3.3k
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