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

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.

unplaced scaffolds reference based assembly cnv
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updated by lakhujanivijay lakhujanivijay • written by chevivien chevivien

1 answer

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.

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written by lakhujanivijay lakhujanivijay

Thanks for the input.

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written by chevivien chevivien

Welcome, please upvote or accept answer if that really helped you. This will help future visitors looking for answers of related questions.

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written by lakhujanivijay lakhujanivijay

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

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written by reza reza

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