Should unplaced scaffolds in reference genome be used to map newly sequenced genome

Question

[chevivien]

Hii,

Is it in order to map unplaced scaffolds in reference genome against newly sequenced genome when carrying out reference based assembly? Or it is just ok to use placed chromosomes e.g (ch1-chr29 basing on the number of chromosomes in ref genome) . The purpose of the analysis is to obtain BAM files for CNV detection.

Answer 1

[lakhujanivijay]

According to ensembl definition,for unplaced scaffolds, it is not known which chromosome the scaffold belongs to.

Hence, even if you use them for mapping, you will not be able to identify the annotations.

[reza]

of course some organisms with unplaced scoffolds have gff file containing annotation.

[chevivien]

Thanks for the input.

[lakhujanivijay]

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