Suitable Parameters for Intronic Retrotransposon Splicing

[Dario Strbenac]

A recent journal article found an unusual variety of splicing where an exon of a known gene is spliced to a LINE1 retrotransposon in the following intron. So, instead of continuing to splice well-known exons further along the gene, the LINE1 is the end of the gene and is a way for the cell to temporarily wreck the gene transcript. Because there are thousands of copies of LINE1 repeat in the human genome, how should --chimMainSegmentMultNmax and --chimMultimapNmax be set to enable analysis of this weird splicing? What is the definition of the "main chimeric segment" mentioned in the user manual? Would the genomeGenerate stage also need to have all possible exons which have LINE1 in the adjacent intron included in annotations.gtf? Hopefully, there is a way to enable this analysis easily. The Italian researchers used Trinity to assemble transcripts rather than a genomic alignment approach, but I would like to do it a simpler way.

LINE1 are Spliced in Non-canonical Transcript Variants to Regulate T Cell Quiescence and Exhaustion, Nature Genetics, February 2022.