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ratschlab / spladder

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
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Spladder viz issue: PDF dimensions out of allowed range #189

Open balbachs opened 1 year ago

balbachs commented 1 year ago

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