For the junctions, I've attached a file called
Cleanup_Junctions_w_counts.txt.bz2 which contains a list of 67,317
junctions from the Illumina RNA-Seq data that we analyzed in the paper.
The differences in numbers of junctions depend on what set you are
talking about and are represented by different subsets of junctions as
depicted in the Venn diagram in Supplementary Figure 9a of the Graveley
et al paper.  The junctions you want to display  are the 67,317
junctions from the Illumina only set, and match the number of junctions
plotted in the Venn diagram.
The first four columns in the file I've attached are Junction_ID
(format: chr_start_stop), chromosome, start, stop, followed by a read
count and entropy score column for each sample.  In my opinion, it would
be best to provide both numbers.  The read counts are simply the number
of reads observed that map uniquely to that junction, while the entropy
score is a confidence score in how "real" the junction is.  You can have
junctions with high read counts but low entropy scores, and vice versa,
so both numbers are informative.
The samples are labeled in the table using BS numbers which have the
following translations:
BS40	embryos0-2hr
BS43	embryos2-4hr
BS46	embryos4-6hr
BS49	embryos6-8hr
BS54	embryos8-10hr
BS55	embryos10-12hr
BS58	embryos12-14hr
BS62	embryos14-16hr
BS66	embryos16-18hr
BS67	embryos18-20hr
BS71	embryos20-22hr
BS73	embryos22-24hr
BS107	L1larvae
BS111	L2larvae
BS113	L3larvae_12hr_post_molt
BS196	L3larvaePS_1-2
BS200	L3larvaePS_3-6
BS203	L3larvaePS_7-9
BS129	white_prepupae
BS133	WPP_12hr
BS136	WPP_24hr
BS137	pupae_WPP_2d
BS140	pupae_WPP_3d
BS143	pupae_WPP_4d
BS150	adult_male_1d
BS156	adult_male_5d
BS162	adult_male_30d
BS153	adult_female_1d
BS159	adult_female_5d
BS165	adult_female_30d
Cheers,
Brenton R Graveley
UConn Health Center