Question: How to manipulate a gff or gtf file manually?
0
gravatar for Javad
21 months ago by
Javad60
Javad60 wrote:

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 next-gen genome • 1.3k views
ADD COMMENTlink modified 21 months ago by shoujun.gu370 • written 21 months ago by Javad60
3

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.

ADD REPLYlink written 21 months ago by Juke-342.2k

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

ADD REPLYlink written 21 months ago by Satyajeet Khare1.4k
5
gravatar for shoujun.gu
21 months ago by
shoujun.gu370
Rockville/MD
shoujun.gu370 wrote:

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.

ADD COMMENTlink modified 21 months ago • written 21 months ago by shoujun.gu370
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