Question: How to analyse RNA-Seq data with JUST geneID and TPM values
1
gravatar for andorjkiss
4 months ago by
andorjkiss10
United States
andorjkiss10 wrote:

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

dge rna-seq tpm geneid • 251 views
ADD COMMENTlink modified 4 months ago by igor6.5k • written 4 months ago by andorjkiss10
2
gravatar for igor
4 months ago by
igor6.5k
United States
igor6.5k wrote:

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 written 4 months ago by igor6.5k
1
gravatar for jevanveen
4 months ago by
jevanveen20
jevanveen20 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 usegalazy.org

ADD COMMENTlink written 4 months ago by jevanveen20

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

ADD REPLYlink written 4 months 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 4 months ago by andorjkiss10
1

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

ADD REPLYlink modified 4 months ago • written 4 months ago by Kevin Blighe28k

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 4 months ago by andorjkiss10
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