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Question: How to add tdtomato to mouse genome for RNA seq analysis
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Hello all!

I am currently analyzing some RNA seq data derived from mice that express the reporter, tdtomato, under an endogenous promoter. I'd like to get read counts for tdtomato, but obviously it isn't part of the mouse transcriptome, and therefore Salmon doesn't map reads to it.

From what I can figure out on my own, it seems this shouldn't be that hard. Just add the sequence for tdtomato to the mouse transcriptome that I supply to Salmon. And if I want gene level counts, add the tdtomato accession number to my tab delimited transcipt to gene mapping file. Anything else to be done or to look out for? Thanks! Ed

ADD COMMENTlink 22 months ago jevanveen • 20
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That is pretty much about it. Just check afterwards if tdtomato is appearing in your counts files.

ADD REPLYlink 22 months ago
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I wonder if you have handled to do it. I am also interested in counting tdtomato expression in mouse (sc-RNAseq). Thanks!

ADD REPLYlink 9 months ago
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