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config file error in triplet periodicity
23-Jun-2016, 09:20 PM
Post: #1
config file error in triplet periodicity
1) After preparing the samples for riboseqR input, I ran the triplet periodicity tool. It gave the results but along with an error message.
In the history pane, clicking on the results, in the info, the message was:
Read 1130688 items
Calling frames............................done!
Fontconfig error: Cannot load default config file


I am a bioinfo beginner and I am not sure if I need to be concerned about this error.

2) I have 2 wildtype duplicates (W, W) and 2 mutants (M, M).
When I prepare the input files for riboseqr, and then proceed for triplet periodicty, I just get only one plot. Is this ok? Should not I get one plot for wildtype and one plot for mutant?

Thanks in advance.
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24-Jun-2016, 05:57 PM
Post: #2
RE: config file error in triplet periodicity
Dear RiboGalaxy user,
1) You can ignore this Fontconfig error as it is produced in all cases where plots are generated.
2) I think it is normal that you just get one plot but I need to confirm this with a colleague later. In the meantime you can find some information provided by the developers of the riboSeqR tool at these two links: https://www.bioconductor.org/packages/de...boSeqR.pdf and http://bioconductor.org/packages/release...boSeqR.pdf

Kind Regards
jamesp
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04-Jul-2016, 12:47 PM
Post: #3
RE: config file error in triplet periodicity
Hi,

Just to confirm that the Triplet Periodicity tool only generates one plot.

To generate separate triplet periodicity plots for your wildtype duplicates and your mutant duplicates, the best would be to run 'Prepare riboSeqR input' separately for the two sample types. In other words, run 'Prepare riboSeqR input' for your wild type files and then run another 'Prepare riboSeqR input' job for your mutant files.

Hope this explains,

Best Regards,
The RiboGalaxy team
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