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Grep two files: -F flag gives weird output

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# 8  
Old 11-16-2017
Quote:
Originally Posted by Don Cragun
What output do you get from the command:
Code:
grep -E 'MEF|SNV' gene

This gives me following output:
Code:
grep -E 'MEF|SNV' ext_gene_list.txt

Quote:
MEF2C
I'm on Unix:

x86_64 x86_64 x86_64 GNU/Linux

---------- Post updated at 09:22 AM ---------- Previous update was at 09:05 AM ----------

I'm unable to understand why I get output for:
Code:
grep -Ff ext_gene_list.txt no_idea.txt

Quote:
19 19256812 19256812 exonic MEF2B,MEF2BNB-MEF2B nonsynonymous SNV
19 19257646 19257646 exonic MEF2B,MEF2BNB-MEF2B nonsynonymous SNV
no_idea.txt is a tab sep file.

There's no gene with name: "exonic" "MEF2B" "MEF2BNB-MEF2B", "MEF2BNB" "nonsynonymous SNV", "SNV"

So if there's no gene, I should not get any output with the above command. Which baffles me with -F file. I'm not sure when to use -F flag.

[/
# 9  
Old 11-16-2017
Blank lines will match any data, artifacts in ext_gene_list.txt will cause erroneous results.

You could try adding -o for "only print matching part of lines" to see what its matching against.
# 10  
Old 11-16-2017
Quote:
Originally Posted by Corona688
Blank lines will match any data, artifacts in ext_gene_list.txt will cause erroneous results.

You could try adding -o for "only print matching part of lines" to see what its matching against.
Thanks this helped.
I have gene "F2" in gene list that matching against no_idea.txt.

Code:
grep -Ff f1.txt f2.txt

This was matching "F2" against File2.
This User Gave Thanks to genome For This Post:
Corona688
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