|Thread||Thread Starter||Forum||Replies||Last Post|
|trim galore error||JQL||Bioinformatics||23||02-17-2015 11:21 AM|
|Problem calling Fastqc in Trim Galore?||MDeBiasse||Bioinformatics||2||07-06-2014 04:17 AM|
|Trim Galore output issue||shocker8786||Bioinformatics||2||10-09-2013 07:06 AM|
|Do I need to run trim galore even if my reads are of good quality?||genomics_search||Bioinformatics||1||03-06-2013 11:30 AM|
|How to integrate Trim Galore in Galaxy?||sachitad||RNA Sequencing||2||10-19-2012 02:54 AM|
|02-07-2017, 09:39 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, 12:15 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.