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?
-
-
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
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
Comment