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Differential analysis(RiboseqR): Multiple read counts for the same gene identifier
13-Jun-2018, 06:10 PM
Post: #4
RE: Differential analysis(RiboseqR): Multiple read counts for the same gene identifier
Hi,
I'm using ribogalaxy docker and I tried to run a differential translation analysis for my control and treatment samples, that I have put together in the same Prepare RiboSeqR input. I have put both Control and treatment (RiboSeq and RNASeq alignments) to the same Prepare RiboSeqR input. Triplet periodicity gave me a graph for only the control, but Metagene analysis gave me plots for both control and treatment. When I run differential translation I get the following error:
Fatal error: Exit code 1 (Error)
Traceback (most recent call last):
File "/shed_tools/toolshed.ribogalaxy.ucc.ie/repos/ribogalaxy/riboseqr_wrapper/7b9cb1091196/riboseqr_wrapper/riboseqr/difftrans.py", line 150, in <module>
html_file=args.html_file, output_path=args.output_path)
File "/shed_tools/toolshed.ribogalaxy.ucc.ie/repos/ribogalaxy/riboseqr_wrapper/7b9cb1091196/riboseqr_wrapper/riboseqr/difftrans.py", line 70, in get_counts
run_rscript(cmd)
File "/shed_tools/toolshed.ribogalaxy.ucc.ie/repos/ribogalaxy/riboseqr_wrapper/7b9cb1091196/riboseqr_wrapper/riboseqr/difftrans.py", line 20, in run_rscript
output = R(command)
File "/export/tool_deps/rpy2/2.3.10/ribogalaxy/riboseqr_wrapper/7b9cb1091196/lib/python/rpy2/robjects/__init__.py", line 240, in __call__
res = self.eval(p)
File "/export/tool_deps/rpy2/2.3.10/ribogalaxy/riboseqr_wrapper/7b9cb1091196/lib/python/rpy2/robjects/functions.py", line 86, in __call__
return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
File "/export/tool_deps/rpy2/2.3.10/ribogalaxy/riboseqr_wrapper/7b9cb1091196/lib/python/rpy2/robjects/functions.py", line 35, in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in .local(.Object, ...) :
All vectors in '@groups' slot must equal number of columns of '@data' slot.

Any ideas what I'm doing wrong? I'd really appreciate any feedback

Thanks a lot,

Katerina
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RE: Differential analysis(RiboseqR): Multiple read counts for the same gene identifier - Katerina-D - 13-Jun-2018 06:10 PM

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