[maker-devel] genome duplication?
Carson Holt
carsonhh at gmail.com
Mon Feb 2 14:50:02 MST 2015
Anything less than 10kb.
—Carson
> On Feb 2, 2015, at 2:49 PM, Xabier Vázquez Campos <xvazquezc at gmail.com> wrote:
>
> Thanks Carson. Any suggestion on the size limit to separate the short contigs, eg <500 bp
>
> On 03/02/2015 3:36 AM, "Carson Holt" <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> MAKER requires every gene to have at least some evidence support. This is very important for most most eukaryotes as false positive predictions will dominate what is called by snap/augustus. However, it is not such a large problem in fungi because of their high gene density and less frequent introns. Setting keep_preds=1 will maximize sensitivity at the cost of specificity (bad idea in most eukaryotes, but not so much in fungi). I would not be surprised if a bias toward sensitivity is used by most fungi annotation projects with every gene that can be annotated being annotated (even if it does increase false positives). It is a tactic that can work at least in fungi.
>
> Also if the assembly is fragmented, you will be less likely to have evidence support for all genes as the evidence alignments will not meet the % coverage thresholds in the maker_bopts.ctl file. You may want to separate out your shorter contigs, and annotate them separately with more relaxed thresholds for pcov_blast=, pid_blast=, ep_score_limit=, and en_score_limit=.
>
> —Carson
>
>
>> On Jan 31, 2015, at 4:21 PM, Jason Stajich <jason.stajich at gmail.com <mailto:jason.stajich at gmail.com>> wrote:
>>
>> Xabier -
>> FYI - though you probably already compared, those stats are on par with the Hortaea v1 assembly, (we do have an improved Hortaea assembly now and genome size is still same range supporting the duplication hypothesis)
>> Hw version 1 asmbly -
>> N50 9623; Max 71563
>> CEGMA for Hw1
>> #Prots %Completeness - #Total Average %Ortho
>>
>> Complete 196 79.03 - 498 2.54 81.12
>> Partial 228 91.94 - 673 2.95 95.18
>>
>>
>> Mikael - yes - we should compare notes on the models JGI is calling which have little support in MAKER - I am not sure if their pipeline runs with augustus/snap using informant hints though usually they are bringing RNAseq into the mix - I don't know if your approach for reannotation assembled the RNAseq and used it as evidence?
>>
>> We'll be trying to assess some of this when comparisons of proportion of shared genes in the first 1KFG paper so we may be able to say with more certainty of these extra predictions whether they are shared more widely and get a handle on singleton/false positives rates.
>>
>> Jason
>>
>> Jason Stajich
>> jason.stajich at gmail.com <mailto:jason.stajich at gmail.com>
>>
>> On Sat, Jan 31, 2015 at 12:51 AM, Xabier Vázquez Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>> Thanks Mikael,
>>
>> This are the assembly stats as taken from abyss-fac, indeed it isn't a great N50, but it isn't that bad either
>>
>> n n:500 n:N50 min N80 N50 N20 E-size max sum
>> 14277 7099 1185 500 4698 10771 20438 14530 154519 42.68e6
>>
>>
>>
>> 2015-01-31 19:42 GMT+11:00 Mikael Brandström Durling <mikael.durling at slu.se <mailto:mikael.durling at slu.se>>:
>> Hi Xabier,
>>
>>> 31 jan 2015 kl. 05:48 skrev Xabier Vázquez Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>>:
>>>
>>> Hi all,
>>>
>>> One of the fungal genomes I'm annotating is relatively shattered (?), with many contigs/scaffolds and based on CEGMA analysis only may indicate a potential widespread duplication of the genome
>>>
>>> # Statistics of the completeness of the genome based on 248 CEGs #
>>> #Prots %Completeness - #Total Average %Ortho
>>>
>>> Complete 181 72.98 - 365 2.02 67.40
>>> Partial 230 92.74 - 528 2.30 77.83
>>
>>
>> Judging from these figure, you seem to have a very fragmented assembly? What N50 have you reached? According to my experience, assemblies with an N50 below 5-10 times the average gene length tend to give problems in producing good gene sets. Not to say that the gene sets are unusable, but for comparing e.g. gene complements to other species, it will be hard to draw any conclusions when a high proportion of the genes are incomplete.
>>
>>> The expected genome size is relatively low (~42 Mb by abyss-fac) in comparison with Hortaea werneckii (51.6Mb, 23333 genes), a related fungi with nearly 90% of its genes present in at least two copies.
>>> Paper: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071328 <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071328>
>>>
>>> Now to the Maker part... So, as part of the Maker annotation, I trained SNAP and Augustus, and I generated a specific RepeatModeler library. I recorded the predicted outputs from each Maker run (AED, number of predicted proteins and transcripts...). Both Augustus and SNAP used to give quite high number (~19000 and ~23000 respectively) in comparison with the xxx.all.maker.proteins.fasta (about 13600). So, my first question is, how does maker deal with gene duplications? Or is this just a phenomenon given that there is no support from the protein files provided initially to Maker? I've used 4 different protein files for the annotation, could it be that they weren't the best choices? I picked them from the closest relatives and similar environments
>>
>> Unless you by mistake filter out duplicated gene families as repeats with repeat modeler, maker should not care about duplicated genes. However, maker, without keep_preds=1, reports only genes with some kind of support (be it EST or protein homology). This is rather conservative, but if you enable keep_preds, you will get more genes as you have noted. Just for the sake of comparison, I have reannotad more than ten genomes downloaded from JGI, providing MAKER with similar evidence as JGI, and consistently, MAKER is reporting fewer gene models. I have yet to do a more thorough comparison to tell what genes JGI are reporting that don’t appear in the MAKER annotations.
>>
>>>
>>> So, in my last run I turn the keep_preds=1 and the proteins in the xxx.all.maker.proteins.fasta reached to
>>>
>>> Last question regarding the protein files. I download the annotated genomes from the JGI and most of them have two annotation folders "All_models,_Filtered_and_Not" and "Filtered_Models___best__". I've been using the protein files found in the later as I expected to have real evidence and a lower chance of being predicting false genes. Am I right?
>>
>> Yes, I would say so. The FilteredModels have passed through their model selection pipeline, while all_models contains models from all predictors, as well as combinations of predictors and EST evidence.
>>
>> Just some 2 cents of observations of mine,
>> cheers,
>> Mikael
>>
>>>
>>> Thank you in advance,
>>>
>>> Xabier
>>>
>>>
>>> --
>>> Xabier Vázquez Campos
>>> PhD Candidate
>>> Water Research Centre
>>> School of Civil and Environmental Engineering
>>> The University of New South Wales
>>> Sydney NSW 2052 AUSTRALIA
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>>
>>
>>
>>
>> --
>> Xabier Vázquez Campos
>> PhD Candidate
>> Water Research Centre
>> School of Civil and Environmental Engineering
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
>>
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