How to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files for my analysis?
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8 weeks ago
bionewbie • 0

I am trying to perform STAR alignment and I need the reference files for indexing. I would like to know how to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files so that I can use my following code for indexing :

STAR --runMode genomeGenerate \
          --genomeDir ${FILE_PATH}/star_gff_genome_index \
          --genomeFastaFiles ${FILE_PATH}/annotation/Homo_sapiens.GRCh38.dna.primary_assembly.fa \
          --sjdbGTFfile ${FILE_PATH}/annotation/Homo_sapiens.GRCh38.100.gtf \
          --sjdbOverhang 100 \
          --runThreadN 21
RNA reference genome seq STAR • 718 views
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use wget !

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wget http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
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8 weeks ago

http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/

http://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/

Change the links to release 100 if you really want the same annotation version.

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7 days ago
GokalpC ▴ 80

Use the one from GENCODE. That's what the authors also recommend using.

https://www.gencodegenes.org/human/

Check the STAR manual. They refer to the specific versions that you need.

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