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I am having RNA-seq data set for C.Elegans. I do not know which annotation scientists used for naming the genes of it, but I need to search somehow for the ^ERCC and ^mt- genes like specified in the tutorial:

https://www.bioconductor.org/help/workflows/simpleSingleCell/

If I just implement grepl search for the character array of gene names that I have, I am always getting all values FALSE as if there are no spike-ins and mitochindrial genes.

Any suggestion would be greatly appreciated.

Sample gene name from the dataset: WBGene00023193

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The tutorial you linked to does not mention ERCC or mt genes.

Before running grepl or any other search, you should first check your inputs. It looks like you have WormBase gene IDs if all your genes look like WBGene00023193. Therefore, your question is actually how to convert WormBase gene IDs to gene symbols.

Here is one potential solution: https://github.com/WormBase/website/issues/4297

After you convert, you have to make sure that you have ERCC spike-ins in your gene table (probably not) and you mitochondrial genes start with "mt-".

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  • $\begingroup$ Sorry about that, the link was wrong. I updated it $\endgroup$
    – Nikita Vlasenko
    Dec 13, 2017 at 18:54

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