Does loompy take into account mitochrondial genes in loom file output?

[denvercal1234GitHub]

Hi there,

1. For other package like velocyto, there was discussion regarding how mitochondrial genes were not taken into account by default (no mitochondrial genes are included in loom file (bug fixed, velocyto team please check this) velocyto-team/velocyto.py#318). Anyone wouldn't mind commending on the handling of mitochrondial genes for loom file generated by loompy?

2. Also, would anyone mind clarifying the following points regarding the command below?

Thank you so much for your help!

1. 1kPBMC.loom is the name of the file we want to name the output, which will be placed in the working directory
2. What is the "1kPBMC" after "1kPBMC.loom" ?

loompy fromfq 1kPBMC.loom 1kPBMC human_GRCh38_gencode.v31 metadata.tab ...

My code in the script job: