Hi, I'm following the tutorial to RNA-seq instructions in the biostars handbook and I've reached the stage in section I.6 "The differential expression" where I am downloading deseq2.r and running it.
curl http://data.biostarhandbook.com/books/rnaseq/code/deseq2.r > ~/bin/deseq2.r,
made it executable
chmod +x ~/bin/*.r,
activated the stats environment
conda activate stats
and then ran
to see if it works. However, instead of getting the error message that the handbook says I should expect:
Error: The experimental design must be specified as NxM Execution halted
, I am instead getting
-bash: deseq2.r: command not found.
As expected, when I later try to use deseq2.r to perform a differential analysis, I get the same error message about the command not being found.
Does anybody have any advice on why this might be happening? Thanks in advance!