Changes between Version 47 and Version 48 of SOPs/qc_shortReads


Ignore:
Timestamp:
10/29/18 11:36:55 (6 years ago)
Author:
gbell
Comment:

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  • SOPs/qc_shortReads

    v47 v48  
    7979To check if the SRA sample has paired reads or not, go to the [https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browser SRA Run browser], enter the sample ID, and look in the table under "Layout".
    8080
    81 To get paired reads into separate files, use a command like
    82 
    83 ''**fastq-dump --split-files SRR060751.sra**''
     81To get matched paired reads into separate files, use a command like
     82
     83''**fastq-dump --split-3 SRR060751.sra**''
     84
     85This works the same as using the "--split-files", but "--split-3" puts unpaired reads (if any) into a third file.
    8486
    8587You can ask for gzipped output instead of typical fastq: