This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to manipulate a gff or gtf file manually?

Hello,

I want to manipulate a gtf file manually. I can do this with text editors like gedit. It works very well with small genomes like bacterial genomes but when it comes to big genomes (like human genome) It is slow and it needs high amount of memory to load the annotation file. Is there another feasible way to manipulate annotation files?

Thanks

rna-seq genome next-gen
• 6,730 views • link
updated by shoujun.gu shoujun.gu • written by Javad Javad

What kind of manual manipulation are you doing ? It is not really the kind of file that we like to modify manually... I load huge genome into text editor without any problem using "sublime". I guess using "atom" it will work well too.

• 0 views • link
written by Juke34 Juke34

I use awk grep from command line. You can head your commands before you write any files.

• 0 views • link
written by Satyajeet Khare Satyajeet Khare

1 answer

It's depend on how you want to manipulate your file. For simple modification, linux command line should work. For more sophisticated job, you probably need to use R or Python/Pandas.

And avoid using any text editor to do it manually, since its error prone and may mess up with the file format.

• 0 views • link
written by shoujun.gu shoujun.gu

Log in to answer this question.

More posts like this