Sequencing Reference
Basic Rules for References
- All genomes and references should be put into
/public
directory, which is a SATA SSD with 1T capacity. - If you build an index, please always make sure to put it into the
corresponding directory
.Eg. You build up a hisat2 index using the mm10 genome. You should put the index folder under the
hisat2
directory, name itmm10
at the same time - Please always attach a file describing the parameters or data source link (shell script file preferred) in the same directory. Also, reflect on the folder name briefly.
Eg. If you are going to build a STAR index for T2T with personalized parameters. The folder name should be like
T2T_CHM13v2.0_149
- After building the index or downloading the genome, please update it on this website. Asking the Administrator to change the directory owner to
root
and permission to755
.
Directory Structure
/public
├─ reference/
│ ├─ genomes
│ │ ├─ mm10
│ │ │ ├─ .fa.gz
│ │ │ ├─ .gtf.gz
│ │ │ ├─ RefSeq.bed
│ │ │ └─ RepeatMasker.bed
│ │ ├─ hg38
│ │ │ └─ ...
│ │ └─ ...
│ ├─ STAR
│ ├─ bwa
│ ├─ hisat2
│ ├─ bowtie2
│ ├─ cellranger
│ └─ rsem
└─ ...
Genome | .fa | .gtf | RefSeq | RepeatMasker | STAR | bwa | hisat2 | bowtie2 | cellranger | rsem |
---|---|---|---|---|---|---|---|---|---|---|
T2T-CHM13v2.0 |
||||||||||
hg38 |
||||||||||
hg19 |
||||||||||
mm39 |
||||||||||
mm10 |
✅ | ✅ | ✅ | ✅ | ✅ | |||||
mm9 |
||||||||||
rn6 |
Common Storage Requirement
Fasta+gtf: 4G STAR: 29G bwa: 5G bowtie2: 4G cellranger: 15G rsem: 1G
Download Genomes
-
Where you wish to store files.
-
Insert
ensembl
into the path after thedomain name
before you paste. Note for downloading fromensemblgenomes
sites useensemblgenomes
rather thanensembl
.