RESOURCES

Software

SpliceTools, a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing.  Available through web interface at splicetools.org and by download at https://github.com/flemingtonlab/SpliceTools.

SpliceTools resource files:

• rMATS differential splicing files
  • CC15
  • indisulam_and_ms023
  • NMD_factor_kd
  • RBP_kd
• hg38 transcript annotation BED file
  • hg38.bed

SpliceV for visualizing coverage of and publication quality printing of linear and backsplice junctions.  The software is available for download at https://github.com/flemingtonlab/SpliceV.

TRIMD for transcriptome resolution through integration of Iso-Seq, RNA-Seq, and deepCAGE data.  TRIMD scripts can be found at https://github.com/flemingtonlab/TRIMD.

Genome Annotations

EBV genome annotation files for Next Generation Sequence Analysis.

Inverted Akata fasta and fasta index files for building reference genomes. 

Inverted Akata GTF file for quantitation.

Inverted Akata BED file with additional features such as origins of replication, repeats, microRNAs, etc., for visualization in IGV.