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

David

input de salmon deseq2 rna-seq • 119 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by david.morse0
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 152 users visited in the last hour