How to analyse RNA-Seq data with JUST geneID and TPM values

Question

[andorjkiss]

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

Answer 1

[igor]

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.

Answer 2

[jevanveen]

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

[andorjkiss]

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

[andorjkiss]

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.

[Kevin Blighe]

Another relevant thread in relation to this: https://support.bioconductor.org/p/91218/

[andorjkiss]

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.