Error in Galaxy using Deseq2 "Error in data.frame(..., check.names = FALSE) :"

Question

[Johan Largo]

Hello everyone

How are things going?

Currently, I am processing ARN-seq data using Galaxy. I would like to observe the differential expression between controls and cases. For that, I follow the following steps:

I did a quality check of my library first (obviously) Second, I used HISAT2 for reference genome mapping. Third, I used Stringtie for quantization.

StringTie output there are tabular files in which you can see two columns (gene_id and count)

I don't know, but when I use Deseq2 for the differential expression and input the tabular files into the application, I get the following error:

Error in data.frame(..., check.names = FALSE) :
  arguments imply differing number of rows: 20414, 21980, 21991, 22263, 21480, 20114, 23050, 23557, 22336, 21024, 21702, 21263, 22859, 18976
Calls: get_dese

I hope you please tell me what I am doing wrong or if my input files need to be reviewed.

Note: I am new to using Galaxy and Deseq2

Answer 1

[swbarnes2]

I'm not sure anyone can help you without examining your files..can you at least confirm that all the stringtie outputs have the same number of genes? At first glance, I'd guess that error message means they do not.

[Johan Largo]

Hi, sorry for the delay but I made a mistake in my workflow. The bug was fixed by following the recommendations in the Stringtie manual. Thank you anyway.