Question: how to select longest isoform per gene in gtf
0
gravatar for reza
2.3 years ago by
reza210
Iran
reza210 wrote:

hi everyone

i downloaded a gff file for a vertebrate and converted it to gtf format using gffread. i want to use the gtf file to creat database for SnpEff. Now i am going to choose and maintain single isoform per gene (longest isoform) in gtf file.

anyone can advise me to do this?

thanks in advance

annotation gtf gene • 2.3k views
ADD COMMENTlink modified 2.3 years ago by A. Domingues2.1k • written 2.3 years ago by reza210
3
gravatar for A. Domingues
2.3 years ago by
A. Domingues2.1k
Dresden, Germany
A. Domingues2.1k wrote:

Using the cgat toolset it can be accomplished with:

cgat gtf2gtf --method=filter --filter-method=longest-transcript 

It is a very rich set of tools, so have a look at what else it does because it will make your like easier.

ADD COMMENTlink written 2.3 years ago by A. Domingues2.1k
0
gravatar for EagleEye
2.3 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

Hi, the following script is used to get longer gene/isoform (start and end) from GTF. You can modify this script to solve your task,

ADD COMMENTlink written 2.3 years ago by EagleEye6.4k
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