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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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'GENCODE comprehensive' gene annotation #42

Open emattei opened 4 years ago

emattei commented 4 years ago

Hi, I was wondering if it will be possible to use the 'GENCODE comprehensive catalog' as an option to run SQuIRE. Is RefSeq been chosen for a specific reason? Like shown here http://www.biomedcentral.com/1471-2164/16/S8/S2, the GENCODE comprehensive contains more annotation and covers more genomic regions which sounds ideal for TEs quantification purposes.

Would SQuIRE work with such annotation?

Thanks