Question: Difference b/w primary and alternate genome assembly ?
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sunnykevin97 • 50 wrote:
HI
Can some one give better explanation of primary and alternate genome assembly ?
The organism I'm working has only "primary assembly" can I use this assembly for my data analysis work?
Need suggestions!
NCBI's assembly model is described on this page. If a RefSeq assembly is available for your organism then you should use that for your (unspecified above) analysis.
The primary assembly contains only 26 Chromosomes (25 + mtDNA). The unplaced scaffolds (23) information was missing in the genome assembly. Can I use this as a ref genome for mapping transcriptome ? suggestions!
Unless you are specifically interested in alternate haplotypes/unplaced scaffolds you can use the primary assembly.