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I am using Drop-seq_tools to analyze scRNA-seq in a similar way of this paper. I am using the same data (GSE97930) to get used to Drop-seq_tools.

On the GEO repo the authors provide the relevant code (GSE97930_README.txt). However, one tool used in the script is missing: TagReadWithGene.

The latest version of Drop-seq_tools does not have such method (as it should be provided by this library), and there is no version history for the whole package, so I cannot download previous versions.

The best matches for the missing method are TagReadWithGeneExon and TagReadWithInterval. In the methods of the cited paper they say:

Reads that mapped to intronic or exonic regions of genes as per the GENCODE gene annotation were recorded.

I think that in this case the tool to use should be TagReadWithInterval since the other one should consider only exons.

I cannot find any other documentation about the tools. Do you know/already encountered this problem?

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As per this response from Drop-seq_tools team, at the moment intronic regions cannot be annotated and TagReadWithGeneExon should be used instead.

However, in the version of the public repository:

TagReadWithGeneExonFunction is the old code, for people who want the more simple tagging methodology and rely on it for 3rd party tools, and TagReadWithGeneFunction, which for your purposes replaces TagReadWithGeneExon. [...] You’ll see additional options to extract expression for CODING, UTR, INTRONIC reads [...]

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