lift-over hg19 to GRch38

Question

[kanwarjag]

I am trying to convert 450 K methylation coordinates (Single C location) of given hg19 to GRCH38 following suggestions in previous posts (GRCh37/38(NCBI) vs hg19/hg38(UCSC) and Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api))

using default parameters which are-

Minimum ratio of bases that must remap:0.95:

BED 4 to BED 6 OptionsAllow multiple output regions:off Minimum hit size in query:0;

Minimum chain size in target:0 BED 12 OptionsMin ratio of alignment blocks or exons that must map:1.00If thickStart/thickEnd is not mapped, use the closest mapped base:off

However I get an error :

Deleted in new:
    Sequence intersects no chains
Partially deleted in new:
    Sequence insufficiently intersects one chain
Split in new:
    Sequence insufficiently intersects multiple chains
Duplicated in new:
    Sequence sufficiently intersects multiple chains
Boundary problem:
    Missing start or end base in an exon

Here is one line of input;

chr4    54974682    54974682    +

Any suggestion what is wrong?

Thanks

Answer 1

[Pierre Lindenbaum]

the error is "deleted in new"

chr4:54974682-54974682 is part of a genomic contig on hg19 that is not anymore mapped on GRch38 because the new assembly is now better built without including this contig.

[kanwarjag]

I was having around 1Kb region that is strange that all is deleted or modified.