Hi,
I was wondering if someone might be able to shed some light on the "validity" of the unlocalized contigs that are included as part of the UCSC HG19 assembly (not the haplotypes).
In particular, do these contigs reflect:
(a) chromosome segments that are definitely known to exist, and are not already present on the traditional chromosomes, and will in time get localised.
(b) segments that may or may not exist (e.g. their apparent existence might be an artifact of the assembly process), and so may never be localised.
I'm asking because I'm trying to get a feeling for whether it is appropriate to include these in an rna-seq mapping exercise.
Thanks!
I was wondering if someone might be able to shed some light on the "validity" of the unlocalized contigs that are included as part of the UCSC HG19 assembly (not the haplotypes).
In particular, do these contigs reflect:
(a) chromosome segments that are definitely known to exist, and are not already present on the traditional chromosomes, and will in time get localised.
(b) segments that may or may not exist (e.g. their apparent existence might be an artifact of the assembly process), and so may never be localised.
I'm asking because I'm trying to get a feeling for whether it is appropriate to include these in an rna-seq mapping exercise.
Thanks!
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