Has anyone ever tried to use refseq instead of ensembl transcriptome fasta files for RNAseq analysis with Kallisto, pls? Would there be any concern for me to do so?
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I don't see why that'd be a problem...
Quoting from this benchmark paper:
...when conducting research that emphasizes reproducible and robust gene expression estimates, a less complex genome annotation, such as RefGene, might be preferred. When conducting more exploratory research, a more complex genome annotation, such as Ensembl, should be chosen. -
Got it. Thanks!Comment
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