I have used the Stringtie tool successfully to produce transcript assemblies and additional ballgown input files.
I wanted to also try the DeSeq2 tool so I tried to run Stringtie again with the same data and reference with default settings and changed the additional output to Deseq/EdgeR. But the jobs failed due to following error
"Fatal error: Exit code 1 () Traceback (most recent call last): File "/firstname.lastname@example.org/bin/prepDE.py", line 175, in <module> t_dict[t_id].setdefault(s, int(ceil(coverage*transcript_len/read_len))) NameError: name 'coverage' is not defined"
I am using Galaxy on the local server. I don't understand what went wrong this time as the input data is same and I previously ran succesful analysis with the same tool just with different additional output option.
Can someone kindly point out what seems to be the problem?