Hi!
The CLIFinder tool is dedicated to analyze paired-end RNA-seq. THis was the perequisite to efficiently identify L1 chimeric transcripts. Indeed, analyzing single end RNA-seq data will be less efficient since it imposes that the read must overlap the L1/unique sequence junction on a small size sequence (100-150 bp), which is much more challenging!
Hi! The CLIFinder tool is dedicated to analyze paired-end RNA-seq. THis was the perequisite to efficiently identify L1 chimeric transcripts. Indeed, analyzing single end RNA-seq data will be less efficient since it imposes that the read must overlap the L1/unique sequence junction on a small size sequence (100-150 bp), which is much more challenging!