- spladder version: 3.0.2
- Python version: 3.9.5
- Operating System: CentOS 7
Description
I am trying to visualize splicing using the spladder viz command. However, I only get a white PDF. I have checked that there is an alternative splicing event in the spladder output. When I open the PDF, Adobe Reader tells me that "The dimensions of this page are outside the allowed range of values. Certain page content may not be displayed." (translated from German).
I am suspecting that on the HPC system I am using, the PDF renderer might yield incorrect results. Are there certain requirements to generate PDF output?
Of note, PNG output doesn't work either.
Thank you very much!
Sebastian
What I Did
E2F1_drug.difftest_alt_3prime.83114.pdf
spladder viz --range gene ENSG00000101412 --track coverage ctrl:${list_of_ctrl_bams} P_lof:${list_of_P_lof_bams} --track event any --track splicegraph --track transcript --outbase E2F1 --format pdf --test infiles_ctrl_vs_infiles_P_lof any --testdir spladder_out/infiles_ctrl_vs_infiles_P_lof --outdir spladder_out E2F1
Description
I am trying to visualize splicing using the spladder viz command. However, I only get a white PDF. I have checked that there is an alternative splicing event in the spladder output. When I open the PDF, Adobe Reader tells me that "The dimensions of this page are outside the allowed range of values. Certain page content may not be displayed." (translated from German).
I am suspecting that on the HPC system I am using, the PDF renderer might yield incorrect results. Are there certain requirements to generate PDF output?
Of note, PNG output doesn't work either.
Thank you very much!
Sebastian
What I Did
E2F1_drug.difftest_alt_3prime.83114.pdf