Bimodal %GC plot of fastqc output in RNASeq
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):
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.
1 answer
The genome of rice indeed has a bimodal GC content distribution https://pubmed.ncbi.nlm.nih.gov/25527839/ . This unusual property is characteristic of genomes of some monocots.
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Have you checked to make sure that there is no rRNA contamination in your data. Has the data been trimmed?