Question: Exclude non-coding genes
0
gravatar for rhasanvandj
8 weeks ago by
rhasanvandj10
rhasanvandj10 wrote:

Hello, I have HT-Seq read count with around 60000 genes (with ENSEMBLE ID). I only want to keep protein coding genes. How can I remove non-coding genes?

Thanks

rna-seq gene • 163 views
ADD COMMENTlink modified 8 weeks ago by Pierre Lindenbaum131k • written 8 weeks ago by rhasanvandj10
1
gravatar for Pierre Lindenbaum
8 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

go to http://www.ensembl.org/biomart/martview

database: gene / human gene

attribute : gene stable id

gene: -> gene_type "protein coding"

export as a text file

filter your list with grep -w -f coding.txt you_ids.txt

ADD COMMENTlink written 8 weeks ago by Pierre Lindenbaum131k

Thanks a lot Pierre It was awesome and so easy. I just do not understand your last point: "filter your list with grep -w -f coding.txt you_ids.txt"

how should I do this? sorry I am new to this field and not familiar with things and need more explanation.

ADD REPLYlink written 8 weeks ago by rhasanvandj10
1

You can do this through Terminal if you are on a Mac/Linux as grep is used for Unix operating systems.

  1. First cd to the folder/directory your files (the protein coding genes and your list containing the 6000 genes) are in:

    cd /Users/your/directory/

  2. Run the grep command to filter your your_ids.txt (6000 genes file) using coding.txt (list from Ensembl).

    grep -w -f coding.txt your_ids.txt

  3. This will output to terminal, you can save the output to a file with > output.txt

    grep -w -f coding.txt your_ids.txt > output.txt

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by microbiotaiota20

Hello I am using windows system. Is there any method for wimdows?

ADD REPLYlink written 7 weeks ago by rhasanvandj10

Hello, I'm not familiar with Windows. There is the option to install WSL (Windows Subsystem for Linux) which lets you run the above commands on your Windows machine. Perhaps someone else can suggest a better alternative.

ADD REPLYlink written 7 weeks ago by microbiotaiota20
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