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|02-07-2017, 10:39 AM||#1|
Location: Baton Rouge, LA
Join Date: Feb 2017
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:
I think I could use a grep function of some sorts?
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.
|02-07-2017, 01:15 PM||#2|
Location: Walnut Creek, CA
Join Date: Jan 2014
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.