Genome fasta and GTF files #2
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Genome ReferencesThe latest GTF (V43) references from ENCODE are available through here: https://www.gencodegenes.org/human/ We downloaded the top-level, soft-masked fasta and the gtf file from Ensembl. https://useast.ensembl.org/info/data/ftp/index.html TOPLEVELThese files contains all sequence regions flagged as toplevel in an Ensembl schema. This includes chromsomes, regions not assembled into chromosomes and N padded haplotype/patch regions. EXAMPLESToplevel sequences unmasked: Toplevel soft/hard masked sequences: Sequence Type
Download Files# Fasta File
wget https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.toplevel.fa.gz
# Annotations
wget https://ftp.ensembl.org/pub/release-109/gtf/homo_sapiens/Homo_sapiens.GRCh38.109.chr.gtf.gz |
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The genome assembly downloaded from ENSEMBL corresponds to GenBank Assembly ID GCA_000001405.28 which is GRCh38.p13. However, GRCh38.p13 has been replaced by GRCh38.p14 https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/README 
The genome assembly GRCh38.p14 can be downloaded from here from GenBank: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/ The GenBank fasta headers look like this: Using the Ensembl genome fasta the headers look like this: The gtf from Encode has the format: We can do a quick check to see the ENSEMBL and GenBank references. They should be the same. ENSEMBL chromosome names appear to be more appropriate with the GTF from Encode. |
GTF format from ENSEMBL before and after subsetting miRNA sequences. |
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NCBI reference vs. Ensembl reference: NCBI reference has uppercase Ns and ENSEMBL has lowecase Ns (n) when looking at the headers. However, both seem to be soft-masked genomic DNA i.e. all repeats and low complexity regions have been replaced with lowercased versions of their nucleic base. (Screenshots below). Ensembl reference: ENSEMBL GenBank |
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In the pipeline developed in 2018, the genome file used is:
/fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
And the GTF annotation file is:
ENCFF628BVT.gtf
The same gtf file as above can be downloaded from Encode website here:
https://www.encodeproject.org/files/ENCFF628BVT/
There are 12,279 miRNA entries in this gtf file and three types of genomic features: gene, transcript and exons:
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