Liftover vs Ensembl Crossmap

Question

[Thind amarinder]

I converted some hg19 regions to hg38 using UCSC LiftOver and CrossMap ( on Ensembl). For some regions, I found different strand in the output. (for example OR4F29 ensemble-based output shows - stand but incase of liftover it is +)

the eg. output of the Ensembl

1   139310  139379  -   ENSG00000237683 AL627309.1
1   451678  451696  -   ENSG00000235249 OR4F29
1   686655  686673  -   ENSG00000185097 OR4F16
1   924880  924948  +   ENSG00000187634 SAMD11

vs LiftOver (UCSC)

chr1    139310  139379  -   ENSG00000237683 AL627309.1
chr1    451678  451696  +   ENSG00000235249 OR4F29
chr1    686655  686673  -   ENSG00000185097 OR4F16
chr1    924880  924948  +   ENSG00000187634 SAMD11

Here is the input (hg19)

chr1    139310  139379  -   ENSG00000237683 ENSG00000237683 AL627309.1
chr1    367640  367658  +   ENSG00000235249 ENSG00000235249 OR4F29
chr1    622035  622053  -   ENSG00000185097 ENSG00000185097 OR4F16
chr1    860260  860328  +   ENSG00000187634 ENSG00000187634 SAMD11

Why this is the case and which one is correct?

Answer 1

[Emily]

Let's take a look at these loci in a browser. In GRCh37 and GRCh38. The region falls within the contig AL732372.15, which in GRCh37 is shown as AL732372.15 > and in GRCh38 is shown as < AL732372.15 indicating that it has flipped direction. In GRCh37 the forward strand sequence is AGCCCAGTTGGCTGGACCA, in GRCh38 it's TTGGTCCAGCCAACTGGGC; these sequences are reverse complements. The sequence is confirmed on looking at UCSC for GRCh37 and GRCh38, but they don't show the direction of the contig.

[Thind amarinder]

Thanks, That means 4th column, I got in the output has no role, e.g if you have noticed for OR4F29 ensemble-based output shows - stand but incase of liftover it is +

[GenoMax]

@Emily_Ensembl has this important bit in the answer:

The region falls within the contig AL732372.15, which in GRCh37 is shown as AL732372.15 > and in GRCh38 is shown as < AL732372.15 indicating that it has flipped direction.

UCSC seems to have ignored this.