Tximport in usegalaxy

Question

[pragathi.sneha91]

Devon Ryan: Please help in resolving this issue. How to use tximport in usegalaxy to convert transcript ID(DESEQ2-SALMON) to gene ID. I want to get gene ids from the results of deseq2(salmon) . Which GTF should be used for tximport. Iam getting the following error in tximport- 1 Error in tximport(files, type = opt$format, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance) : all(c(abundanceCol, countsCol, lengthCol) %in% names(raw)) is not TRUE when I provide knowngene GTF file and deseq2 tabular format output to tximport

[GenoMax]

Please ask Galaxy related question on their help forum form specific help: https://help.galaxyproject.org/

[antonioggsousa]

Please follow the recommendation made by GenoMax.

As a short comment, I never used tximport in Galaxy, so I don't know how was implemented, but this software and R function was developed to summarize transcript-level estimates obtained for instance with Salmon into gene-level estimates to perform DGE analysis downstream.

Perhaps there is more than one way of using the software, but I always used it by providing the transcript-level estimates obtained with Salmon, by providing the directory of these files, and a tabular text file with 2 columns: transcript id and, the respective, gene id.

So, as far as I know, you can't provide a deseq2 output neither a GTF to tximport. Where did you see that? (can you provide an example)

I would say that you convert first the transcript-level estimates to gene-level and, only then, perform DGE with DESeq2.

Actually the error that you are getting is because not all the columns that appears in the output of Salmon (abundance, counts, length) appears in the input that you provided.

I hope this helps,

António