Hi all,
First time poster, long time reader.
I have a list of genes in a .txt file. This is a simple column of all the genes I want to know more about I also have a flyBaseGene.txt file, a tab delimited file containing information like TSS start, stop, and all the other fun stuff. [My genes of interest match those in flybasegene by simple Ctrl+F]
I've tried for a while running the following command with some variations in Linux with no desired outcome.
grep -F Genes_of_interest.txt flyBaseGene.txt > Pleasework.txt
Please help!!11!11!1!!1!!!!!
•
written
by
Hushus •
you're using
-F, --fixed-strings
Interpret PATTERN as a list of fixed strings, separated by
newlines, any of which is to be matched. (-F is specified by
POSIX.)
you want
-f FILE, --file=FILE
Obtain patterns from FILE, one per line. The empty file
contains zero patterns, and therefore matches nothing. (-f is
specified by POSIX.)
grep -f Genes_of_interest.txt flyBaseGene.txt > Pleasework.txt
better than grep , use join:
join -t $'\t' -1 1 -2 1 <(sort -t $'\t' -k1,1 list1.txt) <(sort -t $'\t' -k1,1 list2.txt)
I have been trying to use various grep commands including like the one below
grep -f myID.txt info.txt > Pleasework.txt
However, i only get one match back (but I know there are more). The match is the last entry in the column.
myID text is: 150002986789
150076978692 etc
in one column
The info.txt is various line with column seperated information: 15028374023487 1 2 4 father
Any pointers to what I am doing wrong thank you Julia
In case anyone has a similar problem, this worked for me:
grep -wFf <(sed 's/\r$//' file1.txt) file2.txt
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This gave me the flybasegene.txt file + the genes of interest listed at the bottom...
put this in bash script:
save as
grep_gene.sh, then: