| | 1 | = ~/gcc/groups/gonl = |
| | 2 | |
| | 3 | Directory structure of data management. On the Groningen cluster that would be target/gpfs2/gcc/groups/gonl |
| | 4 | Permission to read by gonl group, some folders also write. |
| | 5 | |
| | 6 | * /tools |
| | 7 | * symlink to the /gcc/tools folder (except the folders you don't have access too) |
| | 8 | * /resources |
| | 9 | * symlink to the /gcc/resources folder (except the folders you don't have access too) |
| | 10 | * /home |
| | 11 | * one folder per member of this group |
| | 12 | * /general |
| | 13 | * presentations, publications, other stuff |
| | 14 | * /projects |
| | 15 | * /first_batch |
| | 16 | * /rawdata |
| | 17 | * here is a list of fq.gz files |
| | 18 | * /results |
| | 19 | * /alignment |
| | 20 | * here is a list of bam files |
| | 21 | * /stats |
| | 22 | * here is one file per QC tool |
| | 23 | * /snp |
| | 24 | * here is one vcf file per analysis run |
| | 25 | * /logs |
| | 26 | * intermediate_results |
| | 27 | * whatever is needed, will be empty at end of project |
| | 28 | * /rotterdam_550k |
| | 29 | * /rawdata |
| | 30 | * original provided plink or genomestudio |
| | 31 | * /results |
| | 32 | * here the cleaned up genotypes in agreed upon format |
| | 33 | * /logs |
| | 34 | * /groningen_immunochip |
| | 35 | * /rawdata |
| | 36 | * /results |
| | 37 | * /pilot1 |
| | 38 | * /rawdata |
| | 39 | * /alignment |
| | 40 | * symlinks to the raw alignments used -> /first_batch/rawdata/some.aligned.cleaned.bam |
| | 41 | * /result |
| | 42 | * /snp |
| | 43 | * /indel |
| | 44 | * /cnv |
| | 45 | * logs |
