General Information
Name
modENCODE_mRNA-Seq_U_junctions
Species
D. melanogaster
Project type
FlyBase ID
FBlc0000203
Parent Project
Data Provider
Title
Exon junction identification from RNA-Seq assays of D. melanogaster, iso-1 strain, 30 developmental stages.
Accessions
    Overview
    Description
    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.
    Project attributes
    Reagent type
    Key genes
    GO term(s)
    SO term(s)
    Details
    Sample preparation
    Protocol
    Mode of Assay
    Data analysis
    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.
    Comments
    Additional Information
    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)
    Synonyms and Secondary IDs (3)
    Reported As
    Symbol Synonym
    Cleanup_Junctions_w_counts
    modENCODE_mRNA-Seq_U_junctions
    Name Synonyms
    Exon junction identification from RNA-Seq assays of D. melanogaster, iso-1 strain, 30 developmental stages.
    Secondary FlyBase IDs
      References (3)