Hi Folks,
I have a simple question, but haven't been able to find the answer.
I have been mapping intervals from hg19 to GRCh38 using the NCBI remapping tool. When I compare the sequence from the two reference genomes based on the source and mapped position, the nucleotides match as you would expect. However, if the sequence from the hg19 maps to the complementary strand on GRCh38, then sequences don't match up, but are shifted by -1 (after flipping and substituting the complementary base). Which is to say that if I were to request the GRCh38 sequence after add +1 to the start and end position, then I would get matching hg19 and GRCh38 sequence (after flipping and substitution). Is this an artifact of 0-based indexing, and if so, can someone explain to me why this is.
Thanks in advance for any help.
Best,
Andrew