GRCH38 and hg19

Question

[kanwarjag]

I did alignments with hg19 but I tried to use GRCH 38 for annotation but I get lot of undocumented genes like

AC010884.1
AC011366.3
AC011747.3
AC013275.2

Can we really use GRCh38 for hg19 or not at all. Should I be using GRCH37?

Thanks

Answer 1

[[e-mail]]

The reference genome used for alignment should be the same reference genome used for further processing, including annotation.

Consider either using the current aligned file with GRCh37 (hg19) for annotation or perform the alignment again using GRCh38 (hg38) and then you can use GRCh38 (hg38) during annotation.