When human, mouse, zebrafish, roundworm (C. elegans), yeast (S. cerevisiae), and bacteria (salmonella and M. tuberculosis) show up together in one zoo, a manager is suggested.
- Download genome sequence (.fasta). It downloads the
primary_assemblyversion, if not available,toplevelversion is downloaded. - Download annotation (both .gff3 and .gtf).
- Build aligner index.
- Maintain references in a folder structure which is making sense.
git clone [email protected]:Puriney/MrY.git
cd MrY
pip install ./There are 3 common operations:
- install
- list
- delete
yun install --root-dir /path/to/your/zoo \
--species zebrafish \
--assembly GRCz10 \
--org Ensembl \
--release 90 \
--target allMrY will generate a folder named zebrafish under /path/to/your/zoo
to create references for zebrafish of which the assembly name is GRCz10 in
release 90 of Ensembl.
zebrafish/
├── aligner_index
│ ├── bowtie2
│ │ └── Ensembl
│ │ └── GRCz10
│ │ └── release_90
│ │ ├── GRCz10.dna.1.bt2
│ │ ├── GRCz10.dna.2.bt2
│ │ ├── GRCz10.dna.3.bt2
│ │ ├── GRCz10.dna.4.bt2
│ │ ├── GRCz10.dna.rev.1.bt2
│ │ └── GRCz10.dna.rev.2.bt2
│ └── star
│ └── Ensembl
│ └── GRCz10
│ └── release_90
│ ├── chrLength.txt
│ ├── chrNameLength.txt
│ ├── chrName.txt
│ ├── chrStart.txt
│ ├── exonGeTrInfo.tab
│ ├── exonInfo.tab
│ ├── geneInfo.tab
│ ├── Genome
│ ├── genomeParameters.txt
│ ├── Log.out
│ ├── SA
│ ├── SAindex
│ ├── sjdbInfo.txt
│ ├── sjdbList.fromGTF.out.tab
│ ├── sjdbList.out.tab
│ └── transcriptInfo.tab
├── annotation
│ └── Ensembl
│ └── GRCz10
│ └── release_90
│ ├── ensembl.GRCz10.90.gff3
│ ├── ensembl.GRCz10.90.gff3.gz
│ ├── ensembl.GRCz10.90.gtf
│ └── ensembl.GRCz10.90.gtf.gz
└── genome
└── Ensembl
└── GRCz10
└── release_90
├── Danio_rerio.GRCz10.dna.toplevel.fa.gz
├── GRCz10.dna.fa
└── GRCz10.dna.fa.gz -> /path/to/your/zoo/zebrafish/genome/Ensembl/GRCz10/release_90/Danio_rerio.GRCz10.dna.toplevel.fa.gz
Alternatively, more than one species can be installed in the same time:
yun install --root-dir /ifs/data/yanailab/ref \
--species zebrafish roundworm brewer_yeast \
--assembly GRCz10 WBcel235 R64-1-1 \
--release 90 90 90 \
--org Ensembl \
--target all
List available references for specific zibrafish:
yun list --root-dir /path/to/your/zoo \
--species zebrafish \
--assembly GRCz10 \
--org Ensembl \
--release 90
==========
zebrafish-GRCz10-Ensembl-90 was queried:
Genome (.fa): Installed
Annotation (.gtf): Installed
Annotation (.gff3): Installed
Bowtie2: Installed
STAR: Installed
Alternatively, list all available references and a markdown table will be generated.
yun list --root-dir /path/to/your/zoo
| Species | Assembly | Org | Release | Genome (.fa) | Annotation (.gtf) | Annotation (.gff3) | Bowtie2 | STAR |
|---|---|---|---|---|---|---|---|---|
| zebrafish | GRCz10 | Ensembl | 90 | True | True | True | True | True |
| roundworm | WBcel235 | Ensembl | 90 | True | True | True | False | False |
| mouse | GRCm38 | GENCODE | M15 | True | True | True | True | True |
| mouse | GRCm38 | Ensembl | 90 | True | True | True | True | True |
| human | GRCh38 | GENCODE | 27 | True | True | True | True | True |
| human | GRCh38 | GENCODE | 23 | False | True | True | False | False |
| human | GRCh38 | Ensembl | 90 | True | True | True | True | True |
| brewer_yeast | R64-1-1 | Ensembl | 90 | True | True | True | True | True |
Check which GTF and GFF3 files are to be deleted before actually removing them.
yun delete --root-dir /path/to/your/zoo \
--species zebrafish \
--assembly GRCz10 \
--org Ensembl \
--release 90 \
--target task_annotation \
-n
Run above command without -n and actually remove them. Change
task_annotation to all to delete all references of specific zebrafish.
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