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/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 /n/groups/shared_databases/rsem_indexes_bowtie2/hg19.fa /n/groups/shared_databases/rsem_indexes_bowtie2/hg19.n2g.idx.fa /n/groups/shared_databases/rsem_indexes_bowtie2/hg19.3.bt2 /n/groups/shared_databases/rsem_indexes_bowtie2/hg19.transcripts.fa.fai ... /n/groups/shared_databases/bowtie2_indexes/hg19.rev.2.bt2 /n/groups/shared_databases/bowtie2_indexes/hg19.fa /n/groups/shared_databases/bowtie2_indexes/hg19.3.bt2 ... /n/groups/shared_databases/bowtie2_indexes/hg19.1.bt2 /n/groups/shared_databases/bowtie2_indexes/hg19.fai /n/shared_db/hg19/uk/bowtie2 /n/shared_db/hg19/uk/bowtie2/2.2.9 /n/shared_db/hg19/uk/bowtie2/2.2.9/chrUn_gl000233.fa ... /n/shared_db/hg19/uk/bowtie2/2.2.9/chr9_gl000198_random.fa /n/shared_db/hg19/uk/bowtie2/2.2.9/chr6_apd_hap1.fa /n/shared_db/hg19/uk/bowtie2/2.2.9/chr3.fa /n/shared_db/hg19/uk/bowtie2/2.2.9/chr2.fa |
Many of our modules also point to the relevant databases. You can use the module spider command to identify a module of interest, and then to find the appropriate databases. Here is an example for cellranger:
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# look for available cellranger modules $ module spider cellranger # will report all cellranger modules on O2 # get more information on a given cellranger module, # including where to find the relevant databases: $ module spider cellranger/6.0.0 ... Help: For detailed instructions, go to: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger Currently available references: Human reference (GRCh38) is currently found at: /n/shared_db/GRCh38/uk/cellranger/6.0.0/6.0.0/refdata-gex-GRCh38-2020-A Human reference (hg19) is currently found at: /n/shared_db/hg19/uk/cellranger/6.0.0/6.0.0/refdata-cellranger-hg19-3.0.0 Mouse reference (mm10) is currently found at: /n/shared_db/mm10/uk/cellranger/6.0.0/6.0.0/refdata-gex-mm10-2020-A Human/Mouse hybrid reference (GRCh38/mm10) is currently found at: /n/shared_db/GRCh38-mm10/uk/cellranger/6.0.0/6.0.0/refdata-gex-GRCh38_and_mm10-2020-A Human/Mouse hybrid reference (hg19/mm10) is currently found at: /n/shared_db/hg19-mm10/uk/cellranger/6.0.0/6.0.0/refdata-cellranger-hg19-and-mm10-3.0.0 ERCC reference is currently found at: /n/shared_db/misc/cellranger/6.0.0/6.0.0/refdata-cellranger-ercc92-1.2.0 Other references will be added as they release. These paths may be subject to change, so please ensure that they are valid paths before running cellranger against them. If any are missing, please contact rchelp@hms.harvard.edu. |