I would like to run DESeq2 with quant.sf files generated using Salmon quant RNA-Seq transcript abundance analysis. I am trying to do a standard wildtype vs knockout differential gene expression analysis.
The DESeq2 homepage indicates that quant.sf files can be uploaded directly if they are in the proper format indicated here with Name, length, etc in columnized format.
I have uploaded a transcript ID to Gene ID mapping file that looks like this, with the transcript name and gene ID side by side in a .txt file. I have also tried a similar table where the isoform ID of the gene is removed.
My .sf count files have the transcript ID in the A column and the length and reads in the subsequent columns. To start I have been trying one wildtype and one knockout sample to run through DESeq2.
The error message I am receiving is regarding duplicates attached here indicating an issue with replicates.
Is there a quick fix to this solution in my input files? Our lab has quantified using the salmon → galaxy DESeq2 workflow before but my guess is there are updates we are not meeting in our format.
Any help would be greatly appreciated. Thank you.