gtf file for hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta

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Fiona Liang

• August 12, 2023 06:18

Hi all,

I use hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta which download from 

> https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0/chrM;tab=objects?prefix=&forceOnObjectsSortingFiltering=false

to run the mitochondrial pipeline.

I also want to annotate the alignment results to see which gene of mtDNA have mutations. I think .gtf file is necessary to annotate the reference genome.

So, I want to know where is hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta comes from. 

Is it ok for me to extract chrM of gencode.v44.annotation.gtf for annotation of hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta ?

 

Thank you in advance!

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  Gökalp Çelik

  • August 12, 2023 19:15

  Hi again. 

  Mitochondria genome for the task should be compatible with the hg38 gencode annotations therefore gtf file should be ok. 

  Regards.

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