I am working with HeLa cells and want to know how to get cufflinks etc. to 
highlight if a region of the genome is being transcribed that is not in the 
ensembl gtf. I know that cufflinks highlights with class code "j" regions that 
do not match a known gene and therefore may be novel but most of these arise 
from transcription on or near known genes. Does anyone know how to look for 
transcription that is clearly distinct from known genes? This is a wild goose 
chase but worth a peek just in case...

Best Wishes,

Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol

Tel. +44 117 3312058
Fax. +44 117 3312091


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