Question: what is a "Tabular file with Transcript - Gene mapping" in DESeq2?
gravatar for david.morse
7 months ago by
david.morse0 wrote:

I have RNA Seq data from two conditions using a non-model organism. I constructed a trinity assembly from this and then used Salmon to get read counts from both conditions (three replicates). Now I want to find the significant differences, by when I run DESeq2 I get the following error:

Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 11 elements Calls: read.table -> scan

Can I make the tabular file requested from the trinity assembly? I tried the fasta to tabular converter but this did not help.


input de salmon deseq2 rna-seq • 279 views
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by david.morse0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


You'll need to obtain a transcript-to-gene mapping tabular dataset for your non-model organism to use TMP inputs with DeSeq2. This may come from a public source or could be one that you create yourself using an RNA-seq transcript assembly tool (example: Stringtie). This output is not generated by Trinity itself.

Galaxy tutorials with example usage for RNA-seq analysis:

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson25k
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