Use tximport to merge and transform the transcript counts to gene counts
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14 months ago
anasjamshed ▴ 120

I have this data: counts

And I want to convert this into gene counts. How can I do ?

RNAseq gene • 1.3k views
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How is creating a post here and not Googling the first thing you do? Unless you have a specific question and a track of what you've tried and where you're running into difficulties, please consider heavily before you create a new post.

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The data was obtained from salmon run on mouse RNAseq data

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14 months ago
bkleiboeker ▴ 370

What have you tried so far? Googling the exact the title of this post took me to this vignette which looks like what you want to do: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html

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I also went through that tutorial but don't know how to proceed further

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There's literally 2 whole sections for dealing with salmon output files. Unless you ask more specific questions I'm going to assume you are trolling and stop replying.

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I was just confused

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You mention you'd tried something and were confused. When you create a post, mention what exactly you tried and where you stopped and why you stopped. When you try and write it out like that, you'll be able to solve the problem yourself a lot of the times.

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