Genome index 2025

Genomes Available for MMG3320 (Spring 2025)

For the alignment stage, you will need to specify the location of an indexed reference genome. Then during the counting stage you will need to specify the location of the GTF annotation file. The locations to these files can be found on the mmg3320/course_materials folder in the paths specified below.

Information about the Indexed Reference Genomes and GTF

The reference genome have been indexed and are available for the following organisms: human, mouse, thale cress, and rice. The FASTA files for these organisms were downloaded from either Gencode or Ensembl.

Below is a depiction of the folder structure and location for the reference indexes.

Warning

YOU WILL NOT NEED TO MAKE A COPY OF ANY REFERENCE INDEXES IN YOUR HOME DIRECTORY

Simply specify the location of the reference genome/GTF file of interest in your script!

File Paths

GTF & FASTA files

├── Arabidopsis_thaliana.TAIR10.60.gtf
├── Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
├── Homo_sapiens.GRCh38.113.gtf
├── Homo_sapiens.GRCh38.dna.primary_assembly.fa
├── Mus_musculus.GRCm39.113.gtf
├── Mus_musculus.GRCm39.dna.primary_assembly.fa
├── Oryza_sativa.IRGSP-1.0.60.gtf
└── Oryza_sativa.IRGSP-1.0.dna.toplevel.fa

Location of GTF & FASTA files

/gpfs1/cl/mmg3320/course_materials/genome_index_mmg3320/genome_reference

Human Reference Index, GRCh38

├── Homo_sapiens.GRCh38.1.ht2
├── Homo_sapiens.GRCh38.2.ht2
├── Homo_sapiens.GRCh38.3.ht2
├── Homo_sapiens.GRCh38.4.ht2
├── Homo_sapiens.GRCh38.5.ht2
├── Homo_sapiens.GRCh38.6.ht2
├── Homo_sapiens.GRCh38.7.ht2
└── Homo_sapiens.GRCh38.8.ht2

Location of Human Reference Index, GRCh38

/gpfs1/cl/mmg3320/course_materials/genome_index_mmg3320/HISAT2_indexes/Ensembl/Hsapiens_GRCh38

Mouse Reference Index, GRCm39

├── Mus_musculus.GRCm39.1.ht2
├── Mus_musculus.GRCm39.2.ht2
├── Mus_musculus.GRCm39.3.ht2
├── Mus_musculus.GRCm39.4.ht2
├── Mus_musculus.GRCm39.5.ht2
├── Mus_musculus.GRCm39.6.ht2
├── Mus_musculus.GRCm39.7.ht2
└── Mus_musculus.GRCm39.8.ht2

Location of Mouse Reference Index, GRCm39

/gpfs1/cl/mmg3320/course_materials/genome_index_mmg3320/HISAT2_indexes/Ensembl/Mmus_GRCm39

Rice Reference Index, OSativa

├── Osativa_v60.1.ht2
├── Osativa_v60.2.ht2
├── Osativa_v60.3.ht2
├── Osativa_v60.4.ht2
├── Osativa_v60.5.ht2
├── Osativa_v60.6.ht2
├── Osativa_v60.7.ht2
└── Osativa_v60.8.ht2

Location of Rice Reference Index, OSativa

/gpfs1/cl/mmg3320/course_materials/genome_index_mmg3320/HISAT2_indexes/Ensembl/Osativa_IRGSP

Thale Cress Reference Index, TAIR10

├── TAIR10-v60.1.ht2
├── TAIR10-v60.2.ht2
├── TAIR10-v60.3.ht2
├── TAIR10-v60.4.ht2
├── TAIR10-v60.5.ht2
├── TAIR10-v60.6.ht2
├── TAIR10-v60.7.ht2
└── TAIR10-v60.8.ht2

Location of Thale Cress Reference Index, TAIR10

/gpfs1/cl/mmg3320/course_materials/genome_index_mmg3320/HISAT2_indexes/Ensembl/TAIR10_v60

Information about GTF & FASTA files downloaded from Ensembl

Organisms included: Rice, Thale Cress, Human and Mouse

Website:

https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/current/gtf/ https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/current/fasta/

Files:

+ Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
+ Arabidopsis_thaliana.TAIR10.60.gtf.gz 
+ Oryza_sativa.IRGSP-1.0.dna.toplevel.fa.gz
+ Oryza_sativa.IRGSP-1.0.60.gtf.gz

File naming for Ensembl:

Files are consistently named following this pattern:

<species>.<assembly>.<version>.gtf.gz

<species>:       The systematic name of the species.
<assembly>:      The assembly build name.
<version>:       The version of Ensembl from which the data was exported.

gtf : All files in these directories are in GTF format gz : All files are compacted with GNU Zip for storage efficiency.

Toplevel:These 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.

More information about the GTF file

The GTF (General Transfer Format) is an extension of GFF version 2 and used to represent transcription models. GFF (General Feature Format) consists of one line per feature, each containing 9 columns of data.

Fields

Fields are tab-separated. Also, all but the final field in each feature line must contain a value; "empty" columns are denoted with a '.'

seqname   - name of the chromosome or scaffold; chromosome names 
            without a 'chr' 
source    - name of the program that generated this feature, or 
            the data source (database or project name)
feature   - feature type name. Current allowed features are
            {gene, transcript, exon, CDS, Selenocysteine, start_codon,
            stop_codon and UTR}
start     - start position of the feature, with sequence numbering 
            starting at 1.
end       - end position of the feature, with sequence numbering 
            starting at 1.
score     - a floating point value indiciating the score of a feature
strand    - defined as + (forward) or - (reverse).
frame     - one of '0', '1' or '2'. Frame indicates the number of base pairs
            before you encounter a full codon. '0' indicates the feature 
            begins with a whole codon. '1' indicates there is an extra
            base (the 3rd base of the prior codon) at the start of this feature.
            '2' indicates there are two extra bases (2nd and 3rd base of the 
            prior exon) before the first codon. All values are given with
            relation to the 5' end.
attribute - a semicolon-separated list of tag-value pairs (separated by a space), 
            providing additional information about each feature. A key can be
            repeated multiple times.

Attributes

The following attributes are available. All attributes are semi-colon separated pairs of keys and values.

gene_id: The stable identifier for the gene
gene_version: The stable identifier version for the gene
gene_name: The official symbol of this gene
gene_source: The annotation source for this gene
gene_biotype: The biotype of this gene
transcript_id: The stable identifier for this transcript
transcript_version: The stable identifier version for this transcript
transcript_name: The symbold for this transcript derived from the gene name
transcript_source: The annotation source for this transcript
transcript_biotype: The biotype for this transcript
exon_id: The stable identifier for this exon
exon_version: The stable identifier version for this exon
exon_number: Position of this exon in the transcript
ccds_id: CCDS identifier linked to this transcript
protein_id: Stable identifier for this transcript's protein
protein_version: Stable identifier version for this transcript's protein
tag: A collection of additional key value tags
transcript_support_level: Ranking to assess how well a transcript is supported (from 1 to 5)

Information about GTF & FASTA files downloaded from Gencode

Organisms included: Human and Mouse

Website:

https://www.gencodegenes.org/mouse/release_M36.html

Version:

GRCm39/mm39 - version M36
GRCh38/hg38 - version 47

Description of files:

FASTA information Genome sequence, primary assembly (GRCm39)

+ Nucleotide sequence of the GRCm39 primary genome assembly (chromosomes and scaffolds)
+ The sequence region names are the same as in the GTF/GFF3 files

GTF information

+ It contains the comprehensive gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions