Bimodal %GC plot of fastqc output in RNASeq
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4.5 years ago
devbt15 ▴ 30

Dear all, Recently I performed RNASeq 150 bp paired-ends reads in rice (Illumina). I performed fastqc on the fastq files and obtained %GC plots (in the link below):

enter image description here

As shown in the plot, a second bump is observed at 70%. However, fastqc does not suggest any overrepresented sequences or adaptor contamination.

Any suggestions on what these could be?

Regards.

RNA-Seq fastqc %GC Rice Illumina • 960 views
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Please use instructions here to add images : How to add images to a Biostars post

Have you checked to make sure that there is no rRNA contamination in your data. Has the data been trimmed?

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