N could not be mapped to EnsemblID

Mauwsaya · July 17, 2024, 12:19pm

Hi, thanks for the amazing tool!

Even though not many (26) genes could not be mapped, as seen in the log output below, I would still like to be able to check which genes so I can check why. Could this be added to the log?

Thanks,
Maus

1.81839e+00 seconds == WARNING: Not all of your gene identifiers were EnsemblID; 0 were mapped to EnsemblID; 28304 were already EnsemblID; 26 could not be mapped to EnsemblID

Mauwsaya · July 17, 2024, 12:39pm

Excuse me, I found them under “gene_identifier_mapping” in the .json!

danielsf · July 17, 2024, 4:46pm

Great! I’m glad you found that.

For anyone else who encounters this thread, we just added an example Jupyter notebook to the MapMyCells codebase on GitHub that walks users through the detailed contents of the output files produced by MapMyCells.

github.com

AllenInstitute/cell_type_mapper/blob/main/examples/explore_mapping_results.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "8808301b-463d-45b3-bb21-98df7e2f23e8",
   "metadata": {},
   "source": [
    "# Set up environment\n",
    "\n",
    "#### You only need to run the first two cells if your environment has never been set up and had the necessary libraries installed\n",
    "The cell below will install the python libraries necessary to run this notebook"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2fcabbbc-9d6a-49b1-a280-2d25e125a105",
   "metadata": {},
   "outputs": [],
   "source": [

This file has been truncated. show original

(it also walks through the process of creating an h5ad file in python and submitting it to MapMyCells, but that part is less relevant to this thread)

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N could not be mapped to EnsemblID

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