Missing junction

[wcarre]

I am trying to use Splice Launcher on RNASeq data.
We were suspecting a modification of splicing in gene DDX3X. But it seems in the output that the junction we were looking for is not identify in any of the samples. We specify the Mane transcript (ENST00000644876) but the juction corresponding to intron 12-13 in position chrX:41,345,549-41,346,228 is not present in the output file while all the other are :

chrX_41344399_41345179 chrX 41344399 41345179 + forward ENST00000644876 DDX3X 831 1525 676 1067 744 819 1023 681 0 0 0 0 0 0 0 0 Physio 10_11 c.1025 c.1026 0 920.75 8 NA NA NA
chrX_41344399_41345193 chrX 41344399 41345193 + forward ENST00000644876 DDX3X 0 0 0 1 0 0 0 0 0 0 0 0.0937207122774133 0 0 0 0 3AS del_11p(14) c.1025 c.1040 0.0117150890346767 0.125 1 NA NA NA
chrX_41344399_41345403 chrX 41344399 41345403 - forward ENST00000644876 DDX3X 0 0 1 0 0 0 0 0 0 0 0.152091254752852 0 0 0 0 0 SkipEx del_11 c.1025 c.1171 0.0190114068441065 0.125 1 NA NA NA
chrX_41344564_41345179 chrX 41344564 41345179 + forward ENST00000644876 DDX3X 1 5 1 2 0 0 3 0 0.120336943441637 0.327868852459016 0.14792899408284 0.187441424554827 0 0 0.293255131964809 0 5AS ins_10q(165) c.1025+165 c.1026 0.134603918312891 1.5 5 Gamma No NA
chrX_41345246_41345276 chrX 41345246 41345276 + forward ENST00000644876 DDX3X 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NoData Event too complex c.1092 c.1123 0 0.25 1 NA NA NA
chrX_41345308_41345533 chrX 41345308 41345533 + forward ENST00000644876 DDX3X 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 NoData Event too complex c.1154 c.1301 0 0.125 1 NA NA NA
chrX_41345318_41345431 chrX 41345318 41345431 - forward ENST00000644876 DDX3X 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NoData Event too complex c.1164 c.1199 0 0.375 1 NA NA NA
chrX_41345322_41345537 chrX 41345322 41345537 + forward ENST00000644876 DDX3X 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 NoData Event too complex c.1168 c.1305 0 0.25 1 NA NA NA
chrX_41345324_41345375 chrX 41345324 41345375 + forward ENST00000644876 DDX3X 0 0 1 0 2 0 0 0 0 0 0.156494522691706 0 0.232018561484919 0 0 0 3AS ins_11p(28) c.1170 c.1171-28 0.0485641355220781 0.375 2 NA NA NA
chrX_41345324_41345403 chrX 41345324 41345403 + forward ENST00000644876 DDX3X 900 1508 639 1306 862 903 915 810 0 0 0 0 0 0 0 0 Physio 11_12 c.1170 c.1171 0 980.375 8 NA NA NA
chrX_41345324_41345449 chrX 41345324 41345449 + forward ENST00000644876 DDX3X 0 4 3 1 0 0 0 0 0 0.26525198938992 0.469483568075117 0.0765696784073507 0 0 0 0 3AS del_12p(46) c.1170 c.1217 0.101413154484049 1 3 NA NA NA
chrX_41345324_41445307 chrX 41345324 41445307 + forward ENST00000644876 DDX3X 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NoData Outside Transcript c.1170 c.*97589 0 0.125 1 NA NA NA
chrX_41345425_41346300 chrX 41345425 41346300 - forward ENST00000644876 DDX3X 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 NoData Event too complex c.1192 c.1388 0 0.125 1 NA NA NA
chrX_41345431_41346313 chrX 41345431 41346313 - forward ENST00000644876 DDX3X 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 NoData Event too complex c.1198 c.1401 0 0.125 1 NA NA NA
chrX_41346395_41348494 chrX 41346395 41348494 + forward ENST00000644876 DDX3X 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 NoData Event too complex c.1482 c.*776 0 0.125 1 NA NA NA
chrX_41346410_41346493 chrX 41346410 41346493 - forward ENST00000644876 DDX3X 0 2 0 0 0 0 2 2 0 0.182982616651418 0 0 0 0 0.298507462686567 0.388349514563107 3AS ins_13p(11) c.1497 c.1498-11 0.108729949237637 0.75 3 NA NA NA
chrX_41346410_41346504 chrX 41346410 41346504 + forward ENST00000644876 DDX3X 617 1093 460 766 618 627 670 515 0 0 0 0 0 0 0 0 Physio 13_14 c.1497 c.1498 0 670.75 8 NA NA NA
chrX_41346410_41346508 chrX 41346410 41346508 + forward ENST00000644876 DDX3X 0 3 0 2 0 1 2 0 0 0.274473924977127 0 0.261096605744125 0 0.159489633173844 0.298507462686567 0 3AS del_14p(4) c.1497 c.1502 0.124195953322708 1 4 NA NA NA
chrX_41346410_41346566 chrX 41346410 41346566 - forward ENST00000644876 DDX3X 0 2 0 0 0 0 0 0 0 0.182982616651418 0 0 0 0 0 0 3AS del_14p(62) c.1497 c.1560 0.0228728270814273 0.25 1 NA NA NA
chrX_41346414_41346504 chrX 41346414 41346504 - forward ENST00000644876 DDX3X 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0.388349514563107 5AS ins_13q(4) c.1497+4 c.1498 0.0485436893203883 0.25 1 NA NA NA
chrX_41346414_41346991 chrX 41346414 41346991 + forward ENST00000644876 DDX3X 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NoData Event too complex c.1497+4 c.1749 0 0.125 1 NA NA NA
chrX_41346549_41346896 chrX 41346549 41346896 - forward ENST00000644876 DDX3X 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 NoData Event too complex c.1542 c.1654 0 0.125 1 NA NA NA
chrX_41346622_41346858 chrX 41346622 41346858 + forward ENST00000644876 DDX3X 1025 1292 733 1361 1051 1091 1258 924 0 0 0 0 0 0 0 0 Physio 14_15 c.1615 c.1616 0 1091.875 8 NA NA NA

The output file from Star seems to identify this junction and IGV also show this juction.

[wcarre]

Thanks for your help and for the patch you provided us with.
There is still a problem with DDX3X but for other junctions.
Before the patch the Splicelaucher representation of the gene was :

after the patch we have this

So exons 2 to 4 are not identify despite the fact that the junction are present in the STAR alignment.

[raphaelleman]

Sorry for the very long delay of my answer, the new version of SpliceLauncher (version 3) must corrected this error. This last was due to annoatation error when two different genes overlapping on similar genomic coordinates. I advice you to re-install SpliceLauncher and re-generate new references.