Changes between Version 9 and Version 10 of SOPs/qc_SRA


Ignore:
Timestamp:
09/21/20 15:52:01 (4 years ago)
Author:
gbell
Comment:

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  • SOPs/qc_SRA

    v9 v10  
    33**SRA** (for Sequence Read Archive) is a NCBI binary format for short reads.
    44
    5 It's thoroughly described in the [[http://www.ncbi.nlm.nih.gov/books/NBK47528/|SRA Handbook]]
     5'''Contents'''
     6  * [#one Downloading and processing one NCBI SRA sample at a time]
     7  * [#multiple Downloading and processing multiple NCBI SRA samples]
     8
     9This task is thoroughly described in the [[http://www.ncbi.nlm.nih.gov/books/NBK47528/|SRA Handbook]]
    610
    711SRA files can be downloaded as compressed fastq in a web browser using [[https://ewels.github.io/sra-explorer/|SRA Explorer]].
    … …  
    913Processing SRA files requires the [[https://ncbi.github.io/sra-tools/|NCBI SRA Toolkit]], which is installed on our systems.
    1014
    11 === Downloading and processing one NCBI SRA sample at a time ===
     15=== [=#one Downloading and processing one NCBI SRA sample at a time] ===
    1216
    1317NCBI short-read files can be
    … …  
    6064}}}
    6165
    62 === Downloading and processing multiple NCBI SRA samples ===
     66=== [=#multiple Downloading and processing multiple NCBI SRA samples] ===
    6367
    6468To download a list of SRR files (such as for all of the samples of a data series) from NCBI, use NCBI's 'prefetch'.