Question: quality control (ribo-seq)
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gravatar for andreiareis1987
3 months ago by
andreiareis198730 wrote:

Hi there,

I am starting with Ribo-seq analysis, never did it before and i am in part of the quality control. I have been analyzing NGS data for a few years now but like i said never Ribo-seq and i am getting some results in fastqc that i never seen that! I already search in internet for some similiar results, but no sucess. I wondering if someone did some analysis or some paper that i can read i would be much thankful.! see down the plots from multiqc, gc content and duplication levels

plot1

plot2

Thanks in advance Andreia

quality control ribo-seq • 204 views
ADD COMMENTlink modified 12 weeks ago by Biostar ♦♦ 20 • written 3 months ago by andreiareis198730

Hi Andreia,

I never worked with ribo-seq data but did you check if those 'weird' plots are caused by some contamination from reads mapping to rRNA

ADD REPLYlink written 3 months ago by andres.firrincieli1.1k

Thanks Andres, I tested removing the rRNA and mtRNA (i didnt have tRNA sequences for hg38 ..., but anyway, just a checking with rRNA) and the GC plot didnt change! :/

Andreia

ADD REPLYlink written 12 weeks ago by andreiareis198730

You might find something useful at https://riboviz.org/. Looks to me like it might have a massive over-representation of a small number of sequences. See if there is anything in over-represented sequences that you can blast. I assume you've checked for primer dimers?

ADD REPLYlink written 12 weeks ago by i.sudbery11k
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