Question: How to analyse RNA-Seq data with JUST geneID and TPM values
gravatar for andorjkiss
26 days ago by
United States
andorjkiss10 wrote:


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

dge rna-seq tpm geneid • 146 views
ADD COMMENTlink modified 26 days ago by igor6.0k • written 26 days ago by andorjkiss10
gravatar for igor
26 days ago by
United States
igor6.0k wrote:

There is a recent discussion on this topic here:

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 written 26 days ago by igor6.0k
gravatar for jevanveen
26 days ago by
jevanveen10 wrote:

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

ADD COMMENTlink written 26 days ago by jevanveen10

Thanks, I'll check it out. But my sense of DESeq2 is that one needed the total counts...

ADD REPLYlink written 26 days ago by andorjkiss10

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 written 25 days ago by andorjkiss10

Another relevant thread in relation to this:

ADD REPLYlink modified 25 days ago • written 25 days ago by Kevin Blighe19k

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 written 24 days ago by andorjkiss10
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