Ben Weisburd

Until this is merged into the official repo, I've merged it into my fork @ https://github.com/bw2/SpliceAI so it can be used @ https://spliceailookup.broadinstitute.org/

this isn't well documented, but I'm pretty sure TRF .dat files have 1-based start coords.

and I'm just basing this on the dat files being off-by-one in IGV. I never did find docs for this.

What I ended up using was ``` def tree_envelops_interval(t, i): return any(ti.contains_interval(i) for ti in interval_tree.overlap(i)) ```

I ran into similar errors with `rule_filter.py` (in my case it was `ImportError: Missing required dependencies ['pandas']`) For me, it turned out the order of the installation steps mattered. The...

Hi @SophieCandille, apologies for the delay on this. I'm still not sure about the answer and need to trace it back through the code stack.

Hi @SophieCandille , through discussions with colleagues (particularly Heather Zimmermann), I learned that SpliceAI assigns the "0" position to the first nucleotide of the exon for acceptors and the last...

Thanks for reporting this! I thought I had checked the different orientations, but see that I missed that one. It should be fixed now if you hard-refresh the page (command-shift-R...

I think the donor loss score is being masked correctly because the +16bp position is not at an annotated splice site. The masking behavior of the donor/acceptor gain scores seems...

Could you please share additional examples?