how can I get annotated events?

[mhjiang97]

hello, Thank you for your detailed codes. However I got a question. I'd like to know if I can directly get which alternative splicing event is annotated in the gtf according to the output files? If not, what should I do to figure out all the annotated alternative splicing in the output files? Thanks a lot!

[mhjiang97]

could you please show me where the file like "merge_graphs_intron_retention_C2.anno_only.pickle" is in the output directory? Or how can I create a file like that? in pancanatlas_code_public/alt_splice/event_stats_sub/plot_event_stats_tcga.py, I found this:

 ### load annotation index
is_anno_tcga = cPickle.load(open(os.path.join(paths.basedir_as_sub, 'merge_graphs_%s_C%i.anno_only.pickle' % (event_type, CONF)), 'r'))

Does this file having suffix ".anno_only.pickle" contain the annotated alternative splicing events? Thank you very much!