Summarizing Trim Galore Output

[scottr08]

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

[Brian Bushnell]

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.

[scottr08]

Hey Brian,

Thanks for that fix. It worked perfectly!


Scott