Question

Does strange fastQC GC content report cause a problem for WES analysis?

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5.7 years ago

maria2019 ▴ 250

I have paired-end WES reads and looking at the forward and the reverse reads with FastQC for QC, they both show and unusual GC content distribution (Figure is attached for R1) even after adaptor contamination. Will this cause a problem for my WES analysis? If yes, how can I solve it? GC content:

fastQC WES GC content • 2.1k views

ADD COMMENT • link updated 5.7 years ago by JC 13k • written 5.7 years ago by maria2019 ▴ 250

score 2 · Answer 1 · 2019-03-26

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5.7 years ago

JC 13k

If this is WES, you can expect a deviation for your curve, think on codon usage preference ...

ADD COMMENT • link 5.7 years ago by JC 13k

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Aw I see your point. Thank you

ADD REPLY • link 5.7 years ago by maria2019 ▴ 250