Help with TPM values

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1

Hi!

I’m trying to do gene expression analysis via TPM values only to check for variation since I have data for multiple samples but no replicates. Is there a way to calculate this for the entire data set on galaxy? Or a tutorial? I know the manual calculation only…

I’ve already done Deseq2/STAR analysis and limma.
Or how i can use Stringetie to do this?

I’m a very new user so this would be really helpful. Thanks.

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Welcome, @amglu

Just to clarify:

  1. The experiment has multiple samples
  2. Each sample has just one replicate
  3. You want to compare those single replicates to each other, using TMP values.

The differential expression tools all require sample replicates, so I’m not sure how you performed DESeq2 or Limma with this same data.

You can explain more, but I’m also going to post some links to tutorials that you might want to review, too. Maybe these are things you would be interested in trying, or they will help to frame your question in terms of “what would you like to do differently” from these?

Thanks and we can certainly follow up more. I’m curious about what you are doing manually the most. If that was in R or some notebook, you can do those in Galaxy too. And if it through some other tool, maybe we host that tool or can suggest a similar tool. :slight_smile:

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Hi Jenna,
I ran both using the data from different samples. However, as expected, there were barely any differentially expressed genes. I wanted to use TPM to be able to check for the variation and was following the “Reference-based RNA-Seq data analysis” but they just said that deseq2 was more efficient. I was trying to do this manually through R but I got lost and wanted to know if there was a way to do it through galaxy. I saw a previous post about calculating TPM through HIISTAT values but I was not able to generate them from this. I will look through the links you posted. Thank you so much,

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