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infrastructure:solu [24.09.2019 18:00] Teemu Kuulasmaa |
infrastructure:solu [14.03.2020 13:58] Teemu Kuulasmaa [Available reference data set] |
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Server is connected to the storage space provided by the [UEF IT Services for Research](https:// | Server is connected to the storage space provided by the [UEF IT Services for Research](https:// | ||
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+ | ### Available reference data set | ||
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+ | All the available reference data sets are provided as-is. They are unmodified copies of the original files. | ||
### iGenomes | ### iGenomes | ||
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+ | URL: [[https:// | ||
Following reference genomes can be found from the ** / | Following reference genomes can be found from the ** / | ||
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^Mus musculus ^Version^ | ^Mus musculus ^Version^ | ||
- | |mm9 | + | |mm9 | |
- | |mm10 | + | |mm10 |
^Rattus norvegicus ^Version^ | ^Rattus norvegicus ^Version^ | ||
- | |rn4 | + | |rn4 | |
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+ | ### gnomAD | ||
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+ | URL: [[https:// | ||
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+ | Following variants can be found from the ** / | ||
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+ | ^Data set ^Version^ | ||
+ | |Exome variants (.vcf.bgz, tbi) | | ||
+ | |Exome calling regions (.interval list) | | ||
+ | |Genome variants (.vcf.bgz, tbi) | ||
+ | |Genome calling regions (.interval list) | | ||
+ | |Structural variants (.vcf.gz, tbi) | | ||
### Applications | ### Applications | ||
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|[Singularity Container](https:// | |[Singularity Container](https:// | ||
- | For the terminal | + | In the terminal, you can see the list of available software packages by command |
+ | 'modul avail' | ||
- | homer/ | + | |
- | bamtools/ | + | |
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- | | + | |
- | | + | blast-plus/2.7.1 |
- | bowtie/1.2 fastx-toolkit/ | + | |
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### Lmod Module Environment | ### Lmod Module Environment |