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Question: How to analyse RNA-Seq data with JUST geneID and TPM values
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Hi,

I have a spreadsheet with the geneIDs and the TPM values only. Is there any software that will analyse this in terms of Differential Gene Expression, possibly GO? Or is this pretty much just a big laundry list?

Thanks, Andor

ADD COMMENTlink 22 months ago andorjkiss • 10 • updated 22 months ago igor 7.7k
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There is a recent discussion on this topic here: https://support.bioconductor.org/p/98820/

A relevant quote:

In my opinion, there is no good way to do a DE analysis of RNA-seq data starting from the TPM values. TPMs just throw away too much information about the original count sizes.

ADD COMMENTlink 22 months ago igor 7.7k
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DESeq2 is probably what you want. It does a fine job of giving you DE genes starting with TPM values generated by Kallisto or Salmon. There's a user friendly interface available (free) at usegalazy.org

ADD COMMENTlink 22 months ago jevanveen • 20
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Thanks, I'll check it out. But my sense of DESeq2 is that one needed the total counts...

ADD REPLYlink 22 months ago
andorjkiss
• 10
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Okay, thanks for the tip on DESeq2. Further to this discussion, if one has the output of SAMSeq (R smar), is there a means to easily visualise this data? I have the following in tabular data (gene_ID; mean_length; mean_eff_length; est_counts; tpm) for disease/non-disease states.

ADD REPLYlink 22 months ago
andorjkiss
• 10
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Another relevant thread in relation to this: https://support.bioconductor.org/p/91218/

ADD REPLYlink 22 months ago
Kevin Blighe
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Yeah, thanks - this is also my feeling - without the FASTQ, we're (I'm) making a lot of assumptions - especially with isoforms and potential non-unique fragment mappings (I didn't analyse the data initially). Thanks All.

ADD REPLYlink 22 months ago
andorjkiss
• 10

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