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YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
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Case Xa/b doesn't show - only "Case Xa" #67

Open olgabot opened 7 years ago

olgabot commented 7 years ago

Description

The cases describing the rejection of different events says the correct outcome of sufficient/insufficient reads but the case lettering is wrong

Steps to Reproduce

  1. Run outrigger psi

Expected behavior:

Cases 10-12 should have "b" for the insufficient junction read cases

notes
Case 10b: Isoform1 with sufficient reads but Isoform2 has 1+ junctions with insufficient reads: There are insufficient junction reads      4357
Case 10a: Isoform1 with sufficient reads but Isoform2 has 1+ junctions with insufficient reads: There are sufficient junction reads       41156
Case 11b: Isoform1 has 1+ junction with insufficient reads but Isoform2 with sufficient reads: There are insufficient junction reads        399
Case 11a: Isoform1 has 1+ junction with insufficient reads but Isoform2 with sufficient reads: There are sufficient junction reads        35165
Case 12b: Isoform1 and Isoform2 each have both sufficient and insufficient junctions: There are insufficient junction reads                  28
Case 12a: Isoform1 and Isoform2 each have both sufficient and insufficient junctions: There are sufficient junction reads                    44
Case 3: All junctions with insufficient reads                                                                                            138580
Case 4: Only one junction with sufficient reads                                                                                          315170
Case 6: Unequal read coverage (one side has at least 10x more reads)                                                                      78678
Case 7: Exclusion                                                                                                                        401051
Case 8: Inclusion                                                                                                                        363210
Case 9: Sufficient reads on all junctions                                                                                                 39482
dtype: int64

Actual behavior: 

notes
Case 10a: Isoform1 with sufficient reads but Isoform2 has 1+ junctions with insufficient reads: There are insufficient junction reads      4357
Case 10a: Isoform1 with sufficient reads but Isoform2 has 1+ junctions with insufficient reads: There are sufficient junction reads       41156
Case 11a: Isoform1 has 1+ junction with insufficient reads but Isoform2 with sufficient reads: There are insufficient junction reads        399
Case 11a: Isoform1 has 1+ junction with insufficient reads but Isoform2 with sufficient reads: There are sufficient junction reads        35165
Case 12a: Isoform1 and Isoform2 each have both sufficient and insufficient junctions: There are insufficient junction reads                  28
Case 12a: Isoform1 and Isoform2 each have both sufficient and insufficient junctions: There are sufficient junction reads                    44
Case 3: All junctions with insufficient reads                                                                                            138580
Case 4: Only one junction with sufficient reads                                                                                          315170
Case 6: Unequal read coverage (one side has at least 10x more reads)                                                                      78678
Case 7: Exclusion                                                                                                                        401051
Case 8: Inclusion                                                                                                                        363210
Case 9: Sufficient reads on all junctions                                                                                                 39482
dtype: int64

Versions

$ outrigger --version
outrigger 1.0.0dev
$ uname --all
Linux tscc-login2.sdsc.edu 2.6.32-642.6.1.el6.x86_64 #1 SMP Wed Oct 5 00:36:12 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux