DEseq2 Error in read.table

Hi all,
I’m trying to run DESeq2 with Sailfish files. I have two factors (three files for each factor) and I’m running the program with my own gene mapping file. I have been getting the below error:

Error in read.table(tx2gene, header = hasHeader) :
more columns than column names
Calls: get_deseq_dataset -> read.table

Has anyone seen this? I’m not quite sure what the problem is.

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Hi @ramarro,

the DESeq2 tool in Galaxy can work with count files that may or may not have a header line.
If your file starts with

Name	Length	EffectiveLength	TPM	NumReads

you need to select Files have header? -> Yes.

For data from sailfish you need to select
Choice of Input data -> TPM values
Program used to generate TPMs > Sailfish
and then you need to provide the GTF/GFF file or Tabular file with Transcript-ID to Gene-ID mapping.
This should be the same file you used as input to sailfish.

Finally note that the successor software to Sailfish is Salmon, which is also available in Galaxy.

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Hi @mvdbeek,

Thank you for sharing this information. Unfortunately, these are all the settings that used in my original input, with one exception. I do not have a GTF/GFF file, but I made my own Tabular gene mapping file based off of the RNA reference that I used in the Sailfish program.

I originally tried to generate my count files using Salmon. For some reason, I got an error anytime I used Salmon, so I went Sailfish. Are you familiar with the particular read.table error that I got from the program?

Thank you,


Can you submit a bug report using the bug icon ?

I was able to solve the issue. It was related to the format of the gene mapping file.

Thank you for your assistance.