ExtractFeature

[于振朋]

Hi, judy

Now I have one multiple species MAF file and reference GFF3 file. I want to extract all mRNA sequence, generating Output each mRNA region in a distinct file. And, how to know the gene name for this mRNA.

Could you give me the example of script. 

Thank you.

[Julien Y. Dutheil]

Hi,

Have a look at this book chapter: https://link.springer.com/protocol/10.1007/978-1-0716-0199-0_2

You will find an example script doing what you want there.

As for getting the gene name, I'm afraid this is not straightforward: maffilter does not do that automatically (because the way it is encoded may vary significantly from a GFF to another). The best way is to output minimal statistics of each extracted block, and then use the coordinates of each block and the GFF to extract the corresponding names.

Hope this helps,

Julien.