Exclude non-coding genes
1
0
Entering edit mode
2.1 years ago
Rob ▴ 140

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 • 1.2k views
ADD COMMENT
3
Entering edit mode
2.1 years ago

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 COMMENT
0
Entering edit mode

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 REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1841 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6