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how to select longest isoform per gene in gtf

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

gene gtf annotation
• 8,293 views • link
updated by A. Domingues A. Domingues • written by reza reza

2 answers

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.

• 0 views • link
written by A. Domingues A. Domingues

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,

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written by EagleEye EagleEye

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