Remap GRCh38.p13 to GRCh38
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3 months ago
scheurenm ▴ 10

Hi,

i'm interested in a few Loci located in the hard masked regions of hg38 (like 13p, 14p, 15p) and i mapped my data to GRCh38.p13 and i get spots in the included Haplotypes (like KI270715.1, KN196477.1).

Does anyone know a way to map those to hg38 for creating Heatmaps, ideogram, annotation, ... NCBI Remap just copies those into a new file with the exact same chromosome and region....

map bed genome haplotype • 470 views
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You have features mapped to KI270715.1 and would like to map them to somewhere on the chromosome? That won't be possible because KI270715.1 is an unlocalized-scaffold that's present in GRCh38 as well as GRCh38.p13 (and everything in between).

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That was quite a bad example, but some of the contigs are "just" alts with varying copy number of rDNa, alternative haplotyps or repeats. Therefore they are mappable on unique chr. regions, but while being in those contigs no tool will use them in its workflow (because of hg38 as reference)...

So i'm looking for tool to convert those Alternative loci and repeats like chr13p into chr. Regions of hg38 (because chr13p is hard masked in hg38)

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So you have features mapped to alt loci and you are trying to remap them to main chromosomes? Alt loci are present in all GRCh38 assemblies from GRCh38 to GRCh38.p13 so if you are remapping from one point version of GRCh38 to another, the features will not be "remapped".

However, you can use NCBI Remap service to remap features on alt loci; just use the "Alt loci remap" tab. There's an API and command line tool as well if you need to do this as part of a larger script or automate it.

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3 months ago

A freeze is a freeze. No one maps to anything but the primary assembly, so "mapping to GRCh38.p13" doesn't mean anything other than you may have used a different Ensembl annotation downstream. If you build some kind of an alternative reference using patches then you're essentially on your own island, though this guide may help.