Question: Difference b/w primary and alternate genome assembly ?
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gravatar for sunnykevin97
12 months ago by
sunnykevin97140
sunnykevin97140 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!

assembly genome • 201 views
ADD COMMENTlink written 12 months ago by sunnykevin97140
1

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.

ADD REPLYlink written 12 months ago by GenoMax95k

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!

ADD REPLYlink written 12 months ago by sunnykevin97140

Unless you are specifically interested in alternate haplotypes/unplaced scaffolds you can use the primary assembly.

ADD REPLYlink written 12 months ago by GenoMax95k
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