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/n/shared_db
We started using /n/shared_db for public databases with the launch of the O2 cluster. The databases are organized in this folder structure:
...
mm10/rsem/1.3.0/mm10
Exceptions:
Some databases were assembled by developers and their original folder structure was kept, as in:
Code Block igenome/03032016/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
bcbio databases are databases are maintained by the Harvard Chan Bioinformatics Core , and installed this way:
Code Block bcbio/biodata/genomes/Hsapiens
/n/groups/shared_databases
...
software/genomeVersion/database
Exceptions:
There are some exceptions to the structure, such as: ignome and blastdb
A quick way to find the desired databases:
We have create a text file containing all the database names and paths. You can directly search the species and software:
| Code Block |
|---|
$ grep bowtie2 /n/shared_db/allDatabases.no.bcbio.singularity.rcbio.txt | grep hg19 | less |
You should see (uk means unknown here):
| Code Block |
|---|
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.ump |
...
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.chrlist |
...
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.rev.2.bt2 |
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/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.fa |
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/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.n2g.idx.fa |
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/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.3.bt2 |
...
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.transcripts.fa.fai |
...
... |
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/n/groups/shared_databases/bowtie2_indexes/hg19.rev.2.bt2 |
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/n/groups/shared_databases/bowtie2_indexes/hg19.fa |
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/n/groups/shared_databases/bowtie2_indexes/hg19.3.bt2 |
...
... |
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/n/groups/shared_databases/bowtie2_indexes/hg19.1.bt2 |
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/n/groups/shared_databases/bowtie2_indexes/hg19.fai |
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/n/shared_db/hg19/uk/bowtie2 |
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/n/shared_db/hg19/uk/bowtie2/2.2.9 |
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/n/shared_db/hg19/uk/bowtie2/2.2.9/chrUn_gl000233.fa |
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... |
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/n/shared_db/hg19/uk/bowtie2/2.2.9/chr9_gl000198_random.fa |
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/n/shared_db/hg19/uk/bowtie2/2.2.9/chr6_apd_hap1.fa |
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/n/shared_db/hg19/uk/bowtie2/2.2.9/chr3.fa |
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/n/shared_db/hg19/uk/bowtie2/2.2.9/chr2.fa |
...