grep extract command will remove replicates automatically
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Entering edit mode
17 months ago

Dear all,

I have a file 1, containing many gene ID, and also has replicates for the gene ID. I want to extract the corresponding line from an gff file, I have a script can accomplish this, but this script will remove the replicates automatically, if I don't want to remove the replicates and want to keep the output just like the order in file 1, if there is anyway I could do this...

Here is file 1:

gene14184
gene25736
gene14184
gene8906
gene25736
gene14775
gene4224
gene8906
gene14184
gene24702


Here is the script I am using:

grep -Fwf file1.txt 001660625_genomic.gff > output.txt

RNA-Seq • 326 views
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Entering edit mode

I don't know if I really understand what you want to do, but try this:

(for ID in $(cat file1); do echo -e$ID"\t"$(grep$ID gff1); done;) > output.txt

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17 months ago

Solved!! and Vlookup in excel could also do this. Thanks!!

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Excel could also do this:

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Entering edit mode

Excel can do many things, but once a file gets larger it will crash plus user interaction with it is irreproducable in terms of coding it up in a script. If it helped you this time it is fine but I strongly recommend to learn how to do things outside of Excel. Imagine one of the files was 10Gb in size...what then.