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Old 02-07-2017, 09:39 AM   #1
scottr08
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Location: Baton Rouge, LA

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Default 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
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Old 02-07-2017, 12:15 PM   #2
Brian Bushnell
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Default

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.
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Old 02-07-2017, 12:37 PM   #3
scottr08
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Hey Brian,

Thanks for that fix. It worked perfectly!


Scott
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