Changes between Version 37 and Version 38 of SOPs/mapping


Ignore:
Timestamp:
02/28/17 16:07:24 (8 years ago)
Author:
thiruvil
Comment:

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  • SOPs/mapping

    v37 v38  
    2626fastq-dump can be used to download/fetch the SRA file, or you can download (eg. using wget) the SRA file directly and then run fastq-dump to get the fastq file.  Downloading SRA file directly will avoid changing home dir path for large file (see below).
    2727
    28 As of fastq-dump version 2.8.1, running fastq-dump will require the vdb-config to be setup correctly.  By default, downloaded/cache file is copied to the user home director which is likely to run out of space.  Run ''vdb-config -i'' and use the GUI to enter a different location.  Manually editing the file, $HOME/.ncbi/user-settings.mkfg, doesn't seem to work.  See [[https://ncbi.github.io/sra-tools/install_config.html | NCBI SRA Installation/Config]].  Other alternatives: i) simply symlink the ncbi directory in your home directory to somewhere else with larger storage, or ii) download SRA file directly (eg. using wget) before using wget.
     28As of fastq-dump version 2.8.1, running fastq-dump will require the vdb-config to be setup correctly.  By default, downloaded/cache file is copied to the user home director which is likely to run out of space.  Run ''vdb-config -i'' and use the GUI to enter a different location.  Manually editing the file, $HOME/.ncbi/user-settings.mkfg, doesn't seem to work.  See [[https://ncbi.github.io/sra-tools/install_config.html | NCBI SRA Installation/Config]].  Other alternatives: i) simply symlink the ncbi directory in your home directory to somewhere else with larger storage, or ii) download SRA file directly (eg. using wget) before using fastq-dump.
    2929
    3030{{{