Annotations for use with MISO and sashimi_plot

Question

[mail2steff]

Hello,

I am using MISO for studying alternative splicing sites in Arabidopsis thaliana. MISO needs different types of annotation files namely: Exon-centric annotations, Isoform-centric annotations and Alternative 3’ UTR annotations.

I do not know from where I can download these annotation files for Arabidopsis thaliana. But I tried to index with the gff3 file downloaded from ensembl plants. But when I execute further commands I am getting 0 events:

  summarize_miso --summarize-samples my_output1/ summaries/
    MISO (Mixture of Isoforms model)
    Summarize MISO output to get Psi values and confidence intervals.
    Use --help argument to view options.

    Loading events from: Splicing_events/Sequences/my_output1
    Writing summary to: Splicing_events/Sequences/summaries/summary/my_output1.miso_summary
      - Summarized a total of 0 events.

[64]% compare_miso --compare-samples my_output1/ my_output2/ comparison_output/
Making comparisons directory: /Splicing_events/Sequences/comparison_output
Given output dir: Splicing_events/Sequences/comparison_output
Retrieving MISO files in sample directories...
Computing sample comparison between Splicing_events/Sequences/my_output1 and /Splicing_events/Sequences/my_output2...
  - No. of events in/Splicing_events/Sequences/my_output1: 0
  - No. of events in /Splicing_events/Sequences/my_output2: 0
Creating comparisons parent directory:/Splicing_events/Sequences/comparison_output/my_output1_vs_my_output2
Compared a total of 0 events.

Can anyone guide me ? Thank you