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  • Summarizing Trim Galore Output

    I need to create one .csv or .txt file of all the summaries of each trimming report. I want to create a spreadsheet of my reads so that I can report to my PI. I have 100 trimming reports, and would prefer to not do it by hand. My trimming reports look like this:

    MI9_S76_L001_R1_001.fastq.gz_trimming_report.txt
    MI9_S76_L001_R2_001.fastq.gz_trimming_report.txt

    I think I could use a grep function of some sorts?

    I've tried:

    grep *.txt 'reads' > trim_report12.txt

    And get the following output:

    grep *.txt 'reads' > /work/srile14/trim_report12.txt

    grep: reads: No such file or directory


    Thanks for your help in advance! I'm fairly new to coding.


    Scott

  • #2
    Your command looks fine except you have the order swapped. Should be:

    grep reads *trimming*.txt > trim_report12.txt

    Note that I changed the expression slightly to prevent *.txt from matching trim_report12.txt, which could cause problems.

    Comment


    • #3
      Hey Brian,

      Thanks for that fix. It worked perfectly!


      Scott

      Comment

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