Maker analysis

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Maker analysis

Intikhab
Two questions:

A. make does not show features from external gff.

When we have the following:

1. Prokaryotic genomic sequence masked for RNA (rRNA and tRNA).
2. GenMarkS based combined model (.mod)
3. GenMarkS based predictions (gff)
4. Glimmer predictions (gff)
5. RNA predictions (gff)

What is the best catergory to place the above data?

1 and  2 can go to their obvious place, genome and gmhmm. When I place
Glimmer predictions gff at "pred_gff", it throws an error "Hit should
have a name", although when the gff is placed at "model_gff", there
are no complaints.

Is it a reasonable idea to put 3,4 and 5 combined in one gff and point
to it with "model_gff" or "pred_gff"?

Maker with such a gff taken as "model_gff" and GeneMarkS based model
pointed to "gmhmm" with defined organism_type=prokaryote produces
results where I could not find any source other then maker and
genemark e.g. glimmer based predictions of GeneMarkS based predictions
or RNA predictions.
Any clues why hints from these sources did not show up.

B. How can we gather maker output in Genebank format where mRNA, CDS
and RNA can be defined as features.

Any suggestions?

IA

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Re: Maker analysis

Carson Hinton Holt
Re: [maker-devel] Maker analysis Sorry for the slow reply.  I have been out of town for the last two weeks.

What is the best catergory to place the above data?
1. Prokaryotic genomic sequence masked for RNA (rRNA and tRNA).

genome=

2. GenMarkS based combined model (.mod)

gmhmm=

3. GenMarkS based predictions (gff)

Not needed if supplying .mod file, otherwise pred_gff=

4. Glimmer predictions (gff)

pred_gff=

5. RNA predictions (gff)

Use est_gff if low specificity.  Use pred_gff if high specificity (probably best option for prokaryotes).


B. How can we gather maker output in Genebank format where mRNA, CDS
and RNA can be defined as features.

Try opening the GFF3 file in Apollo then saving as NCBI format.

--Carson

On 6/7/11 1:10 PM, "Intikhab" <intikhab.alam.syed@...> wrote:

Two questions:

A. make does not show features from external gff.

When we have the following:

1. Prokaryotic genomic sequence masked for RNA (rRNA and tRNA).
2. GenMarkS based combined model (.mod)
3. GenMarkS based predictions (gff)
4. Glimmer predictions (gff)
5. RNA predictions (gff)

What is the best catergory to place the above data?

1 and  2 can go to their obvious place, genome and gmhmm. When I place
Glimmer predictions gff at "pred_gff", it throws an error "Hit should
have a name", although when the gff is placed at "model_gff", there
are no complaints.

Is it a reasonable idea to put 3,4 and 5 combined in one gff and point
to it with "model_gff" or "pred_gff"?

Maker with such a gff taken as "model_gff" and GeneMarkS based model
pointed to "gmhmm" with defined organism_type=prokaryote produces
results where I could not find any source other then maker and
genemark e.g. glimmer based predictions of GeneMarkS based predictions
or RNA predictions.
Any clues why hints from these sources did not show up.

B. How can we gather maker output in Genebank format where mRNA, CDS
and RNA can be defined as features.

Any suggestions?

IA

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Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah

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