Question

Assembly to GFF3

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9.7 years ago

navillusol858 ▴ 10

Hello, I have a fasta file which makes up contigs that were assembled by another person, (in total there are 56k contigs). I am wondering what is the best way to use this fasta file in order to create a GFF3 file that I can then use in GBrowse2. What steps should I go through?

RNA-Seq next-gen • 1.8k views

ADD COMMENT • link updated 2.4 years ago by Ram 43k • written 9.7 years ago by navillusol858 ▴ 10

Ram · Accepted Answer · 2014-08-04

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9.7 years ago

cain.cshl ▴ 70

Hi,

You haven't told use what you want to display for these contigs, but I will assume you want to do a sort of typical automated annotation where you'll find genes, transcripts and exons, and whatever other useful stuff you can find. If that's the case, perhaps the best easiest thing to do is to use MAKER.

You can try it out on the web with a few of your contigs to make sure that you like the way it works and then install it yourself, or I believe, you can get a Amazon Web Services version already installed and configured. It is well documented, has a tutorial and is free for academics.

Scott

ADD COMMENT • link updated 2.4 years ago by Ram 43k • written 9.7 years ago by cain.cshl ▴ 70

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Thanks Scott, much appreciated!

ADD REPLY • link 9.7 years ago by navillusol858 ▴ 10

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Another option is running Interscanpro..

ADD REPLY • link 9.7 years ago by 5heikki 11k