mapping file - DESeq2 error

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1

Hello,
I used Salmon for quatification and now I’m trying to run DESeq2. I’m using a mapping file from Transcript ID to GeneID but I get the following error:
reading in files with read.delim (install ‘readr’ package for speed up)
1 2 3 4 5 6
removing duplicated transcript rows from tx2gene
Error in $<-.data.frame(*tmp*, “TXNAME”, value = character(0)) :
replacement has 0 rows, data has 997581
Calls: get_deseq_dataset → $<- → $<-.data.frame

I think my mapping file does not have header bur I do not know how to set header=false and I do not know if that is the real problem.
Would anyone help me with this issue?

2

Hi @caroeweldt

This implies that your mapping file has more than two columns if I am understanding the log.

The mapping file should contain:

  1. No header line
  2. Two columns separated by a single tab
  3. TranscriptIDs in the first column
  4. GeneIDs in the second column
  5. No extra spaces, tabs, or empty lines
  6. The datatype should be assigned as “tabular”. If Galaxy doesn’t guess this datatype with the detecting-the-datatype-file-format function, then there is a format problem.

General help

  • This same mapping file should have been used when running Salmon (parameter = “File containing a mapping of transcripts to genes”)
  • If you used a GTF file instead with Salmon, you should also use that with DESeq2.
  • GFF3 annotation won’t work with these tools – you need either GTF or a tabular mapping. working-with-gff-gft-gtf2-gff3-reference-annotation
  • Make sure that you are inputting the correct output from Salmon == “quant.genes.sf”

I added more tags to your post that link to prior Q&A that helped others, and tutorials are here:

If you need more help – you can either create a share link to your history and post that back, or it might be enough to post back just the first few lines from each of your inputs.

Thanks!