Question: (Closed) FastQC results with abnormal GC content and Overrepresented sequences in RIP-seq datasets
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gravatar for yoyostudents5775
3 months ago by
yoyostudents57750 wrote:

my mouse RIP-seq data have abnormal GC content and the fastqc result in 'GC content' have 2 peaks, first one is about 55% in x axis, y axis is about 500000. the second one as about 85% in axis,y axis is about 1600000, very sharp peak.besides, the GC content each base is not about 25% for A,T,G,C. they looks like electrocardiogram from 0bp to 150 bp. the overrepresented sequence almost G and C. I checks the unmaapped reads in my bam files and blast with NCBI nr database, which shows that these reads were come from mouse. I think it isn't the contaminate with other sequence, I really can't find how this can be? Many thanks for your help~

Links for Fastqc results https://ibb.co/nEveA7 https://ibb.co/jFHbq7

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rna-seq • 167 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by yoyostudents57750

Hello yoyostudents5775!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

Cheers!

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax49k

Strikingly similar.

ADD REPLYlink written 3 months ago by WouterDeCoster29k
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