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							  +
<p>I believe the genomic content for the two is identical, except for the mitochondrial contig.</p>

<p>The contig names are also different. GRCh37 names them `chr1`, `chr2`,,`chr3`, etc, while hg19 just has `1`, `2`, `3`.</p>

<p>Thus you can use the same GTF file for both (excluding mitochondrial, of course) if you do a simple replace operation for the contig names.</p>
