Hello!

I am doing the scanpy pipeline for scRNA quality control analysis: https://github.com/mousepixels/sanbomics_scripts/blob/main/Scanpy_intro_pp_clustering_markers.ipynb

For annotating the group of mitochondrial genes, in the pipeline they use the command:

adata.var['mt'] = adata.var_names.str.startswith('MT-')

where adata.var_names contains the gene names. However, in my dataset the mitochondrial genes do not have a starting pattern such as 'MT-', I have them all in a txt file which goes like the following:

mt-nd3
mt-nd4
mt-nd4l
mt-nd5
mt-nd6
NC_002333.1
NC_002333.10
NC_002333.11
NC_002333.12

My idea was to load the txt in the notebook:

x = open('michondrialgenesDR11.txt', 'r')
mitogenes = x.read()

and now assign these specific genes to adata.var['mt']. However, since they do not have the same start, I am not sure how to assign them all in the variable.

Can anyone help? Thanks a lot.

EDIT - code for when the mitocondrial genes all start with 'MT-' and annotate this group of genes as 'mt'

adata = sc.read_10x_mtx(
    'tutorial_sample/outs/filtered_feature_bc_matrix/',
    var_names='gene_symbols',
    cache=True)
adata.var['mt'] = adata.var_names.str.startswith('MT-')

The problem is for when not all the mitochondrial genes have the same beginning.

In the pipeline, adata.var_names contains the genes of a count matrix that has been converted into adata (AnnData object) which start with MT- (.str.startswith('MT-')). For me, has to contain all the genes that are in the txt file mentioned above.

Thank you!