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Question: what is a "Tabular file with Transcript - Gene mapping" in DESeq2?
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gravatar for david.morse
7 months ago by
david.morse • 0
Canada
david.morse • 0 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.

David
input de salmon deseq2 rna-seq • 279 views
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modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by david.morse • 0
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gravatar for Jennifer Hillman Jackson
7 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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: https://galaxyproject.org/learn/

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson ♦ 25k
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