[maker-devel] Mapping gene names
Shaun Jackman
sjackman at gmail.com
Wed May 14 18:22:37 MDT 2014
I'm using MAKER 2.31.4.
*http://sjackman.ca <http://sjackman.ca>*
On 14 May 2014 17:19, Carson Holt <carsonhh at gmail.com> wrote:
> That should be fixed in the current download? It came up on the mailing
> list a couple of weeks ago. I'll check.
>
> --Carson
>
>
> From: Shaun Jackman <sjackman at gmail.com>
> Reply-To: Shaun Jackman <sjackman at gmail.com>
> Date: Wednesday, May 14, 2014 at 6:06 PM
>
> To: Carson Holt <carsonhh at gmail.com>
> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Mapping gene names
>
> Hi, Carson. I used other_gff to pass the following four-line GFF file of
> Barrnap rRNA annotations through. The output of gff3_merge is quite
> bizarre. See below.
>
> Input:
>
> ##gff-version 3
> 200408_86 barrnap:0.4 rRNA 2171785 2173036 . + . Name=12S_rRNA;product=12S ribosomal RNA
> 200408_86 barrnap:0.4 rRNA 3665772 3666686 . - . Name=16S_rRNA;product=16S ribosomal RNA (partial);note=aligned only 57 percent of the 16S ribosomal RNA
> 200408_86 barrnap:0.4 rRNA 3826637 3827887 . - . Name=12S_rRNA;product=12S ribosomal RNA
> 200408_86 barrnap:0.4 rRNA 4355857 4357119 . + . Name=12S_rRNA;product=12S ribosomal RNA
>
> Output:
>
> ###
> ARRAY(0x7feceb928780)
> ###
> ARRAY(0x7feceaa548a0)
> ###
> ARRAY(0x7feceeb01c60)
> ###
> ARRAY(0x7fecedf6fef8)
> ###
>
> Cheers,
> Shaun
>
> *http://sjackman.ca <http://sjackman.ca>*
>
>
> On 14 May 2014 14:18, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Thanks. Looks interesting. Also since output is already GFF3, you could
>> probably just use it with gff passthrough. It doesn't appear to support
>> eukaryotes though.
>>
>> --Carson
>>
>>
>> Sent from my iPhone
>>
>> On May 14, 2014, at 3:07 PM, Shaun Jackman <sjackman at gmail.com> wrote:
>>
>> Hi, Carson. Perhaps MAKER could integrate Barrnap<http://www.vicbioinformatics.com/software.barrnap.shtml>to predict rRNA.
>>
>> Cheers,
>> Shaun
>>
>> On 4 March 2014 18:33, Carson Holt <carsonhh at gmail.com> wrote:
>>
>>> Trying to call non-coding RNA from ESTs or even sequence homology is
>>> extremely messy (non-trivial problem in most organisms with high false
>>> positive rate), so MAKER for the most part doesn’t even try to do that. It
>>> focuses only on the coding genes. You can now use tRNAscan and snoscan in
>>> the newest version for some non-coding RNA support (those features were
>>> only added a couple of months ago). So just like other prediction tools
>>> (snap, augustus etc.), the primary focus has always been the coding genes.
>>> We’ve only started adding non-coding RNA support recently for iPlant, so
>>> it’s still relatively immature.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>> From: Shaun Jackman <sjackman at gmail.com>
>>> Reply-To: Shaun Jackman <sjackman at gmail.com>
>>> Date: Tuesday, March 4, 2014 at 7:10 PM
>>>
>>> To: Carson Holt <carsonhh at gmail.com>
>>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>> Subject: Re: [maker-devel] Mapping gene names
>>>
>>> Hi, Carson. I set single_length=50, and it worked like a charm. Thanks
>>> for the tip.
>>>
>>> The rRNA genes that are found with est2genome have the feature type set
>>> to *mRNA* and have corresponding *five_prime_UTR*, *CDS* and
>>> *three_prime_UTR* features. Ideally the feature type would be set to
>>> *rRNA* or *tRNA* as appropriate, and would omit the UTR and CDS
>>> features. Is that a feature that you would be interested in adding to
>>> MAKER? The rRNA gene names all start with “rrn” and the tRNA gene names
>>> with “trn”, as is standard, so determining the appropriate type should be
>>> straight forward.
>>>
>>> Thanks again for your help with this. Cheers,
>>> Shaun
>>>
>>>
>>> On 27 February 2014 17:13, Carson Holt <carsonhh at gmail.com> wrote:
>>>
>>>> Set single_exon=1, and the minimum size to a smaller value. I think
>>>> it's set to 250 right now. Also est2genome is looking for ORF, so if there
>>>> is none (as with tRNAs) they probably won't get picked up.
>>>>
>>>> --Carson
>>>>
>>>> Sent from my iPhone
>>>>
>>>> On Feb 27, 2014, at 5:27 PM, Shaun Jackman <sjackman at gmail.com> wrote:
>>>>
>>>> Sorry, ignore my previous question. est_forward also carries forward
>>>> the names of protein evidence and works like a charm. Thank you!
>>>>
>>>> The larger rrn16 and rrn23 genes annotated perfectly, but the smaller
>>>> rrn4.5 and rrn5 and tRNA genes didn’t make it into the all.gff file. They
>>>> are in the blastn output, and in the evidence_0.gff. rrn5 has perfect
>>>> identity, sufficient bits (242 > bit_blastn=40) and sufficient E Value
>>>> (2e-66 < eval_blastn=1e-10). How should I debug which filter is removing
>>>> these hits?
>>>>
>>>> organism_type=prokaryotic
>>>> est2genome=1
>>>> protein2genome=1
>>>> est_forward=1
>>>>
>>>> Cheers,
>>>> Shaun
>>>>
>>>>
>>>> On 27 February 2014 15:17, Shaun Jackman <sjackman at gmail.com> wrote:
>>>>
>>>>> Is there a corresponding protein_forward=1 option to map forward
>>>>> protein names from protein2genome?
>>>>>
>>>>> Cheers,
>>>>> Shaun
>>>>>
>>>>> On 2014-February-26 at 15:45:39 , Carson Holt (carsonhh at gmail.com<//carsonhh at gmail.com>)
>>>>> wrote:
>>>>>
>>>>> Sorry I meant to say prefilter on the score in the mRNA column before
>>>>> passing the gff3 to model_gff.
>>>>>
>>>>> --Carson
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>> On Feb 26, 2014, at 3:50 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>>>>
>>>>> What you can do is run it once with just est_forward=1 and
>>>>> est2genome/protein2genome set to 1. Then take those results, pass them in
>>>>> as model_gff and use the map_forward option to then filter the results
>>>>> based on mRNA score and that would copy names onto new gene under the
>>>>> standard MAKER pipeline. Eventually it’s really supposed to go into a
>>>>> separate tool that will map genes onto new assemblies (but under the hood
>>>>> the tool will just be calling MAKER with certain parameters restricted). I
>>>>> do this because if people commonly use it mixed with things like SNAP I can
>>>>> start to get some very weird behaviors.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>> From: Mikael Brandström Durling <mikael.durling at slu.se>
>>>>> Date: Wednesday, February 26, 2014 at 3:04 PM
>>>>> To: Carson Holt <carsonhh at gmail.com>
>>>>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>>>> Subject: Re: [maker-devel] Mapping gene names
>>>>>
>>>>> It seems that this could be a very useful option in those cases where
>>>>> you have firm a priori knowledge of the placement of ESTs. However, while
>>>>> trying it I note that est_forward implies that the est2genome predictor is
>>>>> turned on, implicitly. Is this necessary for this to work? I’m after the
>>>>> behavior you describe below where exonerate is made to try really hard
>>>>> within a limited region to align an est, but I would not like maker to
>>>>> produce est2genome predictions.
>>>>>
>>>>> In general, I think this maker_coor and est_forward is a feature set
>>>>> that is worthy to be promoted into a documented feature.
>>>>>
>>>>> THanks,
>>>>> Mikael
>>>>>
>>>>> 26 feb 2014 kl. 17:09 skrev Carson Holt <carsonhh at gmail.com>:
>>>>>
>>>>> It will still work without est_forward. It just works a little
>>>>> differently. Keep in mind this was a hidden feature I used to find
>>>>> stubborn or hard to find missing genes after reassembly of a genome.
>>>>>
>>>>> If est_forward is provided, MAKER will parse the database to look for
>>>>> the maker_coor tags early in the pipeline. Then it will create a list of
>>>>> locations to search, and it will search them even if there are no BLAST
>>>>> results to seed the search (normally MAKER gets a BLAST result first and
>>>>> then polishes it with exonerate). So maker_coor=chr1 will cause MAKER to
>>>>> look for a match using all of chr1 as the input to exonerate even when
>>>>> BLAST finds nothing (this is a very very slow search, but can help pick up
>>>>> one or two stubborn genes that don’t remap well). To allow this, MAKER
>>>>> gives exonerate looser matching parameters (i.e. allows for single base
>>>>> pair introns perhaps caused by assembly errors). The logic here is that
>>>>> given the fact that I already told MAKER that with some degree of
>>>>> confidence I expect sequence A to map to to location X, it will try its
>>>>> hardest to make it match.
>>>>>
>>>>> Without est_forward set, the maker_coor= flag still gets read in GI.pm
>>>>> at line 1563, but only after a BLAST alignment has already seeded it to the
>>>>> region (that BLAST result has the information in its description
>>>>> parameter). MAKER will then ignore seeds completely outside of maker_coor.
>>>>> In addition any BLAST seeds that overlap maker_coor will get the search
>>>>> space for alignment polishing adjusted to match maker_coor exactly. Also
>>>>> match parameters for exonerate will not be relaxed as they were with
>>>>> est_forward.
>>>>>
>>>>> As you can see the behavior, is slightly different (because it’s an
>>>>> accidental feature).
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> From: Mikael Brandström Durling <mikael.durling at slu.se>
>>>>> Date: Wednesday, February 26, 2014 at 6:37 AM
>>>>> To: Carson Holt <carsonhh at gmail.com>
>>>>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>>>> Subject: Re: [maker-devel] Mapping gene names
>>>>>
>>>>> That might be a useful and time saving accidental feature. But,
>>>>> reading the code, it seems that I need to supply maker_coor but not
>>>>> gene_id, as well as the configuration option est_forward for this to work.
>>>>> Any occurrences of maker_coor in GI.pm seems to be conditioned on
>>>>> set_forward=1 right?
>>>>>
>>>>> Mikael
>>>>>
>>>>> 26 feb 2014 kl. 14:22 skrev Carson Holt <carsonhh at gmail.com>:
>>>>>
>>>>> Yes. That should work as well as an accidental feature.
>>>>>
>>>>> --Carson
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>> On Feb 26, 2014, at 5:30 AM, Mikael Brandström Durling <
>>>>> mikael.durling at slu.se> wrote:
>>>>>
>>>>> Can this use of maker_coor be used only to hint about the placement of
>>>>> the ests, without affecting the naming of the final genes? Ie if I have a
>>>>> database of EST where I have a priori knowledge of their rough placement,
>>>>> can this placement be given to maker without providing est_forward=1?
>>>>>
>>>>> Thanks,
>>>>> Mikael
>>>>>
>>>>> 26 feb 2014 kl. 01:58 skrev Carson Holt <carsonhh at gmail.com>:
>>>>>
>>>>> There is a way. It’s not a standard option and it’s undocumented, but
>>>>> if you add est_forward=1 to the maker_opts.ctl file, then it will do just
>>>>> that. The option won’t already be there so you’ll have to type it in.
>>>>>
>>>>> There is also a feature designed to work with this option. If you add
>>>>> tags to your fasta headers, those can be used to guide the mapping and
>>>>> naming. For example, gene_id=<some_gene> will ensure different isoforms
>>>>> that share a common gene_id get clustered into the same gene,
>>>>> and maker_coor=chr1:1-10000 in the fasta header will force a particular
>>>>> sequence to only be mapped against chr1 within the range of 1-10000 bp and
>>>>> just using maker_coor=chr1 will force it to only be mapped against chr1.
>>>>>
>>>>> This is an undocumented way to remap genes onto new assemblies using
>>>>> blast alignments of earlier transcript or protein annotations as a guide.
>>>>>
>>>>> —Carson
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> From: Shaun Jackman <sjackman at gmail.com>
>>>>> Reply-To: Shaun Jackman <sjackman at gmail.com>
>>>>> Date: Tuesday, February 25, 2014 at 5:06 PM
>>>>> To: <maker-devel at yandell-lab.org>
>>>>> Subject: [maker-devel] Mapping gene names
>>>>>
>>>>> Hi,
>>>>>
>>>>> I’m annotating a genome using a closely related genome from Genbank,
>>>>> using the .frn (RNA) and .faa (protein) files from Genbank as evidence to
>>>>> annotate my genome. I’ve run Maker, and the annotation seems to have worked
>>>>> well. Is it possible to map the names of the genes from the related species
>>>>> to my annotation? I see the *map_forward* option, which applies to
>>>>> the *model_gff* parameter. Is there a similar option for *est* and
>>>>> *protein*?
>>>>>
>>>>> *maker_opts.ctl*
>>>>>
>>>>> est=NC_123456.frn
>>>>> protein=NC_123456.faa
>>>>> est2genome=1
>>>>> protein2genome=1
>>>>>
>>>>> Thanks,
>>>>> Shaun
>>>>> _______________________________________________ maker-devel mailing
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>
>>>
>>
>
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