About Image output

[avrajit]

• spladder version:3.0.3
• Python version:3.9.15
• Operating System:20.04

Description

I made a visualization of my splicing result by using below command

What I Did

spladder viz -o ./ --track event exon_skip.94
gene_overview.pdf

I like to know is this showing comparison between two sample condition(Group A and B)? or is it showing comparison with reference Genome?

Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.

[akahles]

Dear @avrajit ,

The command as shown just visualizes the alternative event. In your case this is an exon skip. Shown are the inclusion and the exclusion path of the event.

To also add the transcripts annotated for the respective gene (e.g., gene1), you would need to add --track transcript gene1 to your plotting command. You can find more details on how to use the tracks in the Spladder Documentation.

Best,
Andre

[avrajit]

Thanks for your response. I tried that way too. I did that with below command
spladder viz -o ./ --track transcript SPBC36B7.09

And the Error below.

Traceback (most recent call last):
File "/mypath/anaconda3/envs/spladder/bin/spladder", line 8, in
sys.exit(main())
File "/mypath/anaconda3/envs/spladder/lib/python3.9/site-packages/spladder/spladder.py", line 229, in main
options.func(options)
File "/mypath/anaconda3/envs/spladder/lib/python3.9/site-packages/spladder/spladder_viz.py", line 256, in spladder_viz
_parse_gene_info(range_info[1:], genes, gene_names, gids, all_gene_names, options.outdir, options.confidence, options.validate_sg, options.verbose)
File "/mypath/anaconda3/envs/spladder/lib/python3.9/site-packages/spladder/spladder_viz.py", line 79, in _parse_gene_info
assert gid.shape[0] == 1
AssertionError