Bimodal GC curve in FASTQC for plant RNA-seq

Question

[zizigolu]

Hi,

May you please consider this plot of FASTQC and help me to interpret this dual curve in GC content?? I am not sure if this is an error or what to do.

Thank you so much

https://ibb.co/bA1Tzm

[Fabio Marroni]

maybe it is chloroplast? Or some other contaminant?

[zizigolu]

Thank you, might be... I don't know how to be ensured where that come from

[GenoMax]

If most of the data is mapping to the genome of your plant then perhaps no need to be concerned. If a large(r) fraction remains unmapped then take those reads and blast to see what you get.

[Fabio Marroni]

Also, we sometimes filter for chloroplast contaminants using erne-filter. This might be an option (I am never sure if for RNAseq one should filter for chloroplast or not. For DNAseq it helps a lot). However, I fully agree with genomax. If most of the reads are mapped to your target, then it is not your business, maybe the organism has some strange property (i.e. a GC poor region?)

BTW: Can you disclose which plant is that? It has really high GC!

[zizigolu]

Thank you. good reasoning

[zizigolu]

Thank you, makes sense, I should look at the mapping rate