= /target/gpfs2/gcc/groups/gonl = Directory structure of data management. On the Groningen cluster that would be target/gpfs2/gcc/groups/gonl Permission to read by gonl group, some folders also write. * /tools * All software, scripts and tools used to process the data. * Note that all users can install tools of common interest in this shared directory; tools should specify version as typically multiple versions of the same tool cohabit. * /resources * All resources needed for data processing, including genome references, dbSNP releases, etc. * Note that all users can put resources of common interest here. * /home * one private folder per member of this group * /general * presentations, publications, other stuff * /projects * /batchX * /rawdata * here is a list of fq.gz files * /results * /alignment * here is a list of bam files * /stats * here is one file per QC tool * /snp * here is one vcf file per analysis run * /logs * /intermediate_results * whatever is needed, will be empty at end of project * /gwas_data * /rawdata * original provided plink or genomestudio * /results * here the cleaned up genotypes in agreed upon format * /logs * /groningen_immunochip * /rawdata * /results * /pilot * /rawdata * /alignment * symlinks to the raw alignments used -> /first_batch/rawdata/some.aligned.cleaned.bam * /result * /snp * /indel * /cnv * logs * /bgi * /batchX * A set of compressed files containing the plain text data and md5 files for downloading purpose. These are named as follows: timestamp.BGI.batchX.data_type.hg1X.data_format.tar.bz2. All plain text data should be available as a compressed file, including but not limited to: CNV, !InDel, !InDel annotations, SNP, SNP annotation. Some of these are available in multiple formats; see [wiki:BGIDatasets BGI data] page for more explanation about the BGI data and its formats.md5 checksum files is also available for all files. * batchX/bam OR batchX/alignment * The BAM files aligned by BGI * batchX/CNV * CNVs in CNV Detector format. If you want to download for all samples, please download the compressed archive from batchX/ * batchX/indel * !InDels in samtools pileup format. If you want to download for all samples, please download the compressed archive from batchX/ * batchX/indel_annotation * Indels annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/ * batchX/SNP * SNP in SOAPsnp format. If you want to download for all samples, please download the compressed archive from batchX/ * batchX/SNP_annotation * SNP annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/ * batchX/vcf_format/CNV * CNV in VCF format. If you want to download for all samples, please download the compressed archive from batchX/ * batchX/vcf_format/indel * Indel in VCF format. If you want to download for all samples, please download the compressed archive from batchX/ * batchX/vcf_format/SNP * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/ * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/ * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/