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?
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.
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 +
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