Dseq2 tool error

I used DESEQ tool in galaxy for analyzing of my dataset but I exposed with this error and I cannot solve it. an error occurred with dataset: format tabular. database hg38.my history link:

Hi @nicksam

Your job is mostly set up correctly. The message from the tool is stating that the data is too sparse for the chosen parameters.

Screenshots from your error dataset using the i-icon to review the job details. This is always the best place to review what was done.

Inputs/parameters. The files are small, just five lines each. You are losing the first line because of the parameter about a header line being present (your files do not have one).

Job logs These message are usually from the underlying tool, and are worth reviewing.

I think this message is reporting that the data is too sparse to calculate meaningful DE statistics with the chosen parameters. You could try different parameters to see what happens but I think you’ll need to include more genes. The tool is expecting genes from an entire genome.

This is one of the topics at the Bioconductor forum I confirmed my guess against. The authors suggest running the tool on everything, then subsetting after if you are only interested in a few genes. Maybe helps?

Then these are our Galaxy resources:

Thanks for sharing the history, it made the review go fast! Hope this helps :slight_smile:

thanks for consideration jennaj