mt_ann file for MitoDepth

[mairenileath]

Hi,

Could you include the annotation file needed to run MitoDepth in this repository?

Thanks for providing a great tool!

M

[yingzhang121]

I have the same question. The instruction is not helping at all! And the code is not very helpful too.

    for (i in 1:39) {
        if (grepl("TR", mt_ann$gene[i])) {
            rect(mt_ann[i, 2], -2.5, mt_ann[i, 3], -1, col = col[i], 
                border = "white")
            text(location[i], -0.5, mt_ann$gene[i], cex = 0.9)
        }
        else if (grepl("RN", mt_ann$gene[i])) {
            rect(mt_ann[i, 2], -2.5, mt_ann[i, 3], -1, col = col[i], 
                border = "white")
            text(location[i], -0.5, mt_ann$gene[i], cex = 0.9)
        }
        else {
            rect(mt_ann[i, 2], -4, mt_ann[i, 3], -2.5, col = col[i], 
                border = "white")
            text(location[i], -4.5, mt_ann$gene[i], cex = 0.9)
        }
    }

What is this 39-line file? And what do TR and RN mean? In Gencode (GRCh38, v44) MT annotation, it seems to have Mt-tRNA (RN? or TR?), Mt_rRNA and other genes. When I grabbed all the "gene" entries, there are 37 genes.

Please provide an example of the mt_ann file!

Another bug in the code is the "location" variable. It is not defined in the function or elsewhere!