Grep command

Shell Programming and Scripting
1 
  grep -i -f panel_genes.txt hg19_refGene.txt > match.txt

seems to be pulling names the do not exist in the input file (panel_genes.txt) - the output is attached as well (match.txt)

For example, RNF185 or ZNF146 are not genes in the input. I am trying to match the input file genes only and am not sure why it is not. Thank you.

3

match.txt is the output.

4

grep may not be the right tool here... The string "RNF185" contains "NF1", for instance, so grep finds them both.

Are you looking for these strings in any particular column?

5

So whats the content of hg19_refGene.txt - the file within grep is looking for a string "panel_genes.txt".
Also, you're uploading a 'result file' (match.txt) that is alot larger than what you call an input file (panel_genes.txt).

Also, even if i misunderstand the grep command, the result would overwrite the 'more-detailed-looking' match.txt file with a 'row of single strings' compared to its current content.

Phew, translating is hard at times.

6

Basically what I am trying to do is match the exact gene name in the input (panel_genes.txt) with the gene names in column M of the attached hg19_refGene.txt. Thank you.

7

By "column M" I'm guessing you mean "column 13".

awk 'NR==FNR { X[toupper($1)]++ ; next } ; toupper($13) in X' list_file hg19_refGene.txt

Use nawk on Solaris.

Produces 247 results for me, none of which are RNF185.

1 Like
8

@ Corona688 X[toupper($1)] is just enough I think..

9

I am not to familiar with awk and tried the command but got:

awk 'NR==FNR { X[toupper($1)]++ ; next } ; toupper($13) in X' keys hg19_refGene.txt
awk: fatal: cannot open file `keys' for reading (No such file or directory). Thanks.

10

It means there is no file named keys please do check your input.

11

Thank you.