Question: Difference b/w primary and alternate genome assembly ?
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gravatar for sunnykevin97
9 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 • 174 views
ADD COMMENTlink written 9 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 9 months ago by genomax91k

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 9 months ago by sunnykevin97140

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

ADD REPLYlink written 9 months ago by genomax91k
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