Hi all,

What is the difference between GRCh and hg? I have small RNA interaction data with genome like below and they have used hg19 for mapping the reads. I want to use GTF file in Ensemble which is based on GRCh. but I was wondering the hg and GRCh are the same? If not, where can I find the GTF file for the hg19?

    chromosome  start    end      interaction ID  alignment score of target part  strand
    chr2        1.9E+08  1.9E+08  human08246      32                              +
    chr16       5.2E+07  5.2E+07  human04514      32                              -
    chr3        1.1E+08  1.1E+08  human11115      36                              +
    chrM		14360	 14382	  human08122	  34							  +
More information to add (courtesy MatthewP): <a href="https://software.broadinstitute.org/gatk/documentation/article?id=23390#comparison">GRCh37 / hg19 / b37 / humanG1Kv37 - Human Reference Discrepancies</a>

In essence: GRCh37 is identical to hg19 on the main contigs (chr1-24), but differ on chrM.

Kevin