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.
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.
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,
Rosario
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.