grep gene location from gff without removing duplication

Question

[abdullahpadana]

Hi Friends,

i am using grep command for gene location. But grep command automatically remove gene duplication and output file without gene duplication location. actually i need same output file with same pattern of my file. i don't want remove duplication. anybody can guide me about this???

[antonioggsousa]

Please provide an example of data, the output that you need and the code that you've used. Otherwise it is really difficult for us to help you!

António

[abdullahpadana]

I am using this command

grep -f query.file data.file>output.file

but in my output file duplicate gene show only once. but i want output with same sequence pattern of my query.file.

[antonioggsousa]

Show us the first few lines of each file. Use the buttons to customize the answers, inclusive data, like:

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António

[abdullahpadana]

In my query file 1200 gene but I am getting output 882 genes location, but i don't want remove duplication genes location. I need output with same pattern as my query file.

I am using this command

grep -f query.file data.gff> output.file

please guide me

[antonioggsousa]

Give me an example of your query. Is it like:

Gene_1
Gene_2
Gene_3
...

[antonioggsousa]

I just tested your command-line and for me it seems to work. From 50 genes queried I got 1384 lines, with all matches, the genes and mRNA, exons that are the child from the parent gene id. So, I guess it depends on your input, query and output. Without gives us a good description of that, it is impossible to help further.

António

[abdullahpadana]

how i can add data here???? have no option for attachment

[lakhujanivijay]

You need not add the whole file

use head <your_file.gff> and then paste the contents here

[abdullahpadana]

i have 1200 genes in my querry list but i got result 889 , duplication remove. but i don't want remove duplication. i want result as my querry file. Thanks

[antonioggsousa]

Do you have the same query tag, like this gene_1 and gene_1, in your query file. If so, one is enough, because grep will search for one pattern in the whole file.

António