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ratschlab / spladder

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
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Event_pos description unclear #88

Closed Alex-Nesta closed 5 years ago

Alex-Nesta commented 5 years ago

I am looking through the spladder generated HDF5 files from this study: Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

Specifically, I am looking through this file:

merge_graphs_exon_skip_C2.counts.hdf5

you can find it here: https://gdc.cancer.gov/about-data/publications/PanCanAtlas-Splicing-2018

I looked through the spladder wiki and read the file descriptions page.

"event_pos: position of all event exons encoded as start,stop pairs for each event (events are rows, coordinates are columns)"

My question:

Why are there six columns in this matrix? I would expect there to be just two (start and stop). Please let me know what the other two sets of columns are.

Thank you, Alex

Alex-Nesta commented 5 years ago

I finally took some time and was able to figure it out. Col 1 and col 2 are start and stop for the exon before the skipped exon. Col 3 and col 4 are start and stop for the skipped exon. col 5 and 6 are the start and stop for the exon after the skipped exon.