Changes between Version 2 and Version 3 of DataManagement/SftpServer


Ignore:
Timestamp:
Aug 17, 2011 11:39:29 PM (13 years ago)
Author:
laurent
Comment:

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  • DataManagement/SftpServer

    v2 v3  
    11== UMCG SFTP (application20.target.rug.nl) ==
    2 
    32The SFTP server can be used to access most of the data on the UMCG cluster. Please note that since bandwidth is limited, you should only download the minimum files you need and should download compressed version of the files when available (usually available for all plain text files).
    43
    54=== /target/gpfs2/gcc/groups/gonl/sftp/ ===
    6 Root of the SFTP. 
     5Root of the SFTP.
    76
    87=== /target/gpfs2/gcc/groups/gonl/sftp/A4 ===
    … …  
    1110=== /target/gpfs2/gcc/groups/gonl/sftp/BGI ===
    1211Contains all the data coming from BGI, including their variant calls. The data is organized by batch in the batchX subfolders. Each of the subfolders typically contains the following:
    13 * batchX/
    14 ** 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 BGI data page for more explanation about the BGI data and its formats.
    15 ** md5 checksum files for all files.
    16 * batchX/bam OR batchX/alignment
    17 ** The BAM files aligned by BGI
    18 * batchX/CNV
    19 ** CNVs in CNV Detector format. If you want to download for all samples, please download the compressed archive from batchX/
    20 * batchX/indel
    21 ** InDels in samtools pileup format. If you want to download for all samples, please download the compressed archive from batchX/
    22 * batchX/indel_annotation
    23 ** Indels annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
    24 * batchX/SNP
    25 ** SNP in SOAPsnp format. If you want to download for all samples, please download the compressed archive from batchX/
    26 * batchX/SNP_annotation
    27 ** SNP annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
    28 * batchX/vcf_format/CNV
    29 ** CNV in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    30 * batchX/vcf_format/indel
    31 ** Indel in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    32 * batchX/vcf_format/SNP
    33 ** SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
     12
     13 * batchX/
     14   * 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 BGI data page for more explanation about the BGI data and its formats. ** md5 checksum files for all files.
     15
     16 * batchX/bam OR batchX/alignment
     17   * The BAM files aligned by BGI
     18
     19 * batchX/CNV
     20   * CNVs in CNV Detector format. If you want to download for all samples, please download the compressed archive from batchX/
     21
     22 * batchX/indel
     23   * !InDels in samtools pileup format. If you want to download for all samples, please download the compressed archive from batchX/
     24
     25 * batchX/indel_annotation
     26   * Indels annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
     27
     28 * batchX/SNP
     29   * SNP in SOAPsnp format. If you want to download for all samples, please download the compressed archive from batchX/
     30
     31 * batchX/SNP_annotation
     32   * SNP annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
     33
     34 * batchX/vcf_format/CNV
     35   * CNV in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
     36
     37 * batchX/vcf_format/indel
     38   * Indel in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
     39
     40 * batchX/vcf_format/SNP
     41   * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    3442
    3543NOTES:
    36 * Unless specified otherwise, all data is aligned on hg19
    37 * Some of the folder/filenames are inconsistent from one batch to the other. This is because the original names as found on the BGI HD have been kept.
     44
     45 * Unless specified otherwise, all data is aligned on hg19
     46 * Some of the folder/filenames are inconsistent from one batch to the other. This is because the original names as found on the BGI HD have been kept.
    3847
    3948=== /target/gpfs2/gcc/groups/gonl/sftp/pilot ===