How to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files for my analysis?

Question

[bionewbie]

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

[j_eag]

use wget !

[j_eag]

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

Answer 1

[jared.andrews07]

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.

Answer 2

[GokalpC]

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.