[BioC] Can subjunc use splice sites from a reference annotation (i.e. GTF file)?

Ryan C. Thompson rct at thompsonclan.org
Fri Jan 17 01:20:41 CET 2014


I am looking to test out subjunc for aligning my RNA-seq data. I have a 
reference genome and GTF file describing annotated transcripts, with 
splce sites implied by consecutive exons in the same transcript. If 
necessary, I could easily generate a tab-separated file just describing 
all the splice sites in the annotation. Many other spliced aligners can 
use this information to better align reads to known splice forms. Is 
there any way for subjunc to use this information? I don't see any 
option for this in either the command line subjunc program or the 
"align" function in the Rsubread package.

-Ryan Thompson

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