This repository contains code originally developed by Adam English for his article
- Prevalence of alternative splicing choices in Arabidopsis thaliana (2010)
The original article used EST alignments to assess support for alternative splicing variants documented in Arabidospis gene model annotations. The major result of the article was that for most annotated alternative splicing events, one form predominates. Also, when alternative splicing was more frequently observed, it tended to avoid the protein-coding region of genes. However, there were some genes that were highly variable in terms of splicing. These tended to encode genes with function related to splicing or RNA.
Later, we expanded the code base to use RNA-Seq alignments from multiple libraries to report support for annotated alternative splicing choices.
Processing RNA-Seq data for splicing support
- Gene model annotations in BED12 or BED14 format. For examples, see IgbQuickload.org
- Field 4 must contain gene model identifiers that use LOCUS.n naming convention; AltSpliceanalysis uses these identifiers to determine which transcripts belong to which genes
- Junction files generated by tophat or Loraine Lab find_junctions program, one per library
- RNA-Seq alignments in BAM format, one per libary
For an example invocation, see:
- Ann Loraine (firstname.lastname@example.org)
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