Tool: Fungal genome annotation
1
gravatar for bioinformaticssrm2011
4.3 years ago by
India
bioinformaticssrm201180 wrote:

I want to annotate the fungal genome which I got from 454. For that I have predicted the genes using AUGUTUS tool (i have now a output file in gff format) using command-

augustus --species="Homo sapiens" --UTR=on 454AllContigs.fna > output.gff

Now i have gff file, now how can i use this file for annotation. Should i use other tools for annotation ?

Best!

Shashank
 

sequencing tool genome • 3.1k views
ADD COMMENTlink modified 4.3 years ago by matt.sarrasin70 • written 4.3 years ago by bioinformaticssrm201180

There are many other posts on this topic in the forum. 

ADD REPLYlink written 4.3 years ago by dago2.5k
2
gravatar for matt.sarrasin
4.3 years ago by
Canada
matt.sarrasin70 wrote:

Stajich's lab (http://lab.stajich.org/home/people/jason-stajich/) does fungal genome annotation and they use a pipeline that includes PASA (http://pasa.sourceforge.net/). I've never tried it though, but it seems to work quite well for them.

I've been using MAKER http://gmod.org/wiki/MAKER for annotating my fungal species (using RNA-Seq data) and it's worked really well so far. You can feed your gff model directly into it and it'll annotate the genome using a bootstrap gene prediction re-training method.

ADD COMMENTlink written 4.3 years ago by matt.sarrasin70
1

i have installed the MAKER tool, now which command should i use as a for fungal genome annotation ?

i am not able to find any workflow available for MAKER (fungal genome annotaion) as we can see in MOTHUR/QIIME.

 

So, can you tell me the commands which i can use for fungal genome annotation, as you have done work on MAKER.

 

ADD REPLYlink written 4.3 years ago by bioinformaticssrm201180

Here's a great tutorial on how to get it running: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014

And here's further explanation of the config files to control what's happening under the hood: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_control_files_explained

That should give you enough information to get you up and running, and to tweak it to your needs.

ADD REPLYlink written 4.3 years ago by matt.sarrasin70

i tried to follow MAKER, i got an error, i used command (NOTE: i have only fungal genome in fasta format)-

qiime@qiime-VirtualBox:~/Desktop/maker/src$ which maker
/home/qiime/Desktop/maker/bin/maker

qiime@qiime-VirtualBox:~/Desktop/maker/src$ maker -CTL

qiime@qiime-VirtualBox:~/Desktop/maker/src$ genome=454AllContigs.fna
qiime@qiime-VirtualBox:~/Desktop/maker/src$ organism_type=eukaryotic
qiime@qiime-VirtualBox:~/Desktop/maker/src$ est_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ atleast_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ altest_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ protein_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ rm_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ model_pass=0
qiime@qiime-VirtualBox:~/Desktop/maker/src$ pred_pass=1
qiime@qiime-VirtualBox:~/Desktop/maker/src$ other_pass=1
qiime@qiime-VirtualBox:~/Desktop/maker/src$ maker
STATUS: Parsing control files...
WARNING: blast_type is set to 'ncbi+' but executables cannot be located
The blast_type 'ncbi' will be used instead.

ERROR: You have failed to provide a value for 'genome' in the control files.

--> rank=NA, hostname=qiime-VirtualBox

 

ADD REPLYlink written 4.3 years ago by bioinformaticssrm201180

Judging from what I see in your terminal output, it's as if you defined the genome, organism_type, etc. as variables in your shell, rather than in the maker_opts.ctl file. The maker_opts.ctl file is what you're looking to modify because it points Maker to the input files/settings.

ADD REPLYlink written 4.3 years ago by matt.sarrasin70
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