Umbrella record for 30 collections that differ by developmental stage, from 0-2-hr embryos to 30-day adults. Consists of 76-nt single-end and paired-end reads; RNA junctions identified and characterized (presented in GBrowse and in RNA junction reports). Restricted to uniquely aligned reads.
RNA-Seq reads were aligned to databases of predicted splice junctions and to gene models using TopHat, STAR and BLAT. A number of criteria were used to distinguish true splice junctions from false positives. First, only reads with a minimum of 6nt overhang across a junction were considered. Second, an entropy score (which reflects the number of offset reads) was calculated for each splice junction, and only junctions with entropy score >2 in at least two biological samples were considered. The set of junctions was filtered further to exclude junctions when intron length less than 41 nt, junctions that join parologous genes and non-canonical splice junctions not supported by other experimental support.
The associated file (Graveley.2011.1.5-Cleanup_Junctions_w_counts.txt) is mapped to release 5 of the genome assembly and has not been lifted over to release 6.
[Annotation of Drosophila splice junctions](http://intermine.modencode.org/release-33/experiment.do?experiment=Annotation+of+Drosophila+splice+junctions+by+RNA-seq)