Error with combining samples into matrix using abundance_estimates_to_matrix.pl

Question

[nikelle.petrillo]

Hi Everyone. I'm trying to combine my samples into a matrix in order to analyze differentially expressed genes in edgeR, however, I am running into an error that I am not sure what to make of. Any help/advice would be much appreciated! Thank you, Nikelle.

[npetrill@trogdor util]$ perl abundance_estimates_to_matrix.pl --est_method RSEM ~/aligning/aligning3/RSEM.genes.results ~/aligning/aligning4/RSEM.genes.results 

-reading file: /home/npetrill/aligning/aligning3/RSEM.genes.results

-reading file: /home/npetrill/aligning/aligning4/RSEM.genes.results

* Outputting combined matrix.
Error, cannot write file matrix.counts.matrix at abundance_estimates_to_matrix.pl line 168.

[pld]

As Goutham said, it might be permissions. Are you running the script from the directory where it is installed? You may not have permission to write there. Run it from the directory where you want the output to go. You might be able to set the output directory with the --out_prefix option.

In general, you don't need to be in the directory your script is located to run it. Stay where you're "working" and call the script by supplying the path to it, if it isn't already in your $PATH.

Answer 1

[GouthamAtla]

It could be a simple permissions issue. The code says:

my $counts_matrix_file = "$out_prefix.counts.matrix";
open (my $ofh_counts, ">$counts_matrix_file") or die "Error, cannot write file $counts_matrix_file";