[maker-devel] ncRNA support in maker

[Carson Holt]

I’m making a new release this weekend, but if you have access to the devel
version, you can test now.  All changes have been committed tot he
subversion repository.

Thanks,
Carson


On 2/6/14, 4:02 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
wrote:

>Hi Carson,
>
>it’s nice to see all these new features in maker.
>
>I gave the trnascan option a try by enabling it in the config file for
>one of my fungal genomes. It failed though, with this error message:
>
>ERROR: You found a tRNA with an intron! This should not happen
>--> rank=12, hostname=my-mgrid6
>ERROR: Failed while gathering ab-init output files
>ERROR: Chunk failed at level:1, tier_type:2
>FAILED CONTIG:scf_013
>
>ERROR: Chunk failed at level:4, tier_type:0
>FAILED CONTIG:scf_013
>
>I checked the trnascan output
>(scf_013.abinit_nomask.0.eukaryotic.trnascan) in theVoid for that contig,
>and the output seems valid to me:
>
>scf_013         1       189339  189410  Thr     AGT     0       0
>82.83
>scf_013         2       510381  510462  Ser     AGA     0       0
>67.09
>scf_013         3       586886  587000  Leu     CAA     586924  586956
>57.97
>scf_013         4       942166  942069  Leu     AAG     942128  942113
>57.48
>scf_013         5       169102  168993  Leu     TAA     169065  169037
>56.49
>
>
>Hope this can be of some help while debugging. I’ll leave trnascan off
>for now.
>
>thanks,
>
>Mikael
>
>
>10 jan 2014 kl. 22:03 skrev Carson Holt <carsonhh at gmail.com>:
>
>> Hi Mikael,
>> 
>> The options are part of the new MAKER-P integration
>> 
>>(http://www.plantphysiol.org/content/early/2013/12/06/pp.113.230144.abstr
>>ac
>> t).  Additional documentation/tutorials will be forthcoming - probably
>>in
>> a nice wiki page as part of the upcoming GMOD Malaysia courses in
>>February
>> or alternatively with the annual GMOD summer school. The tRNA option is
>> easy enough to turn on (just set trna=1 in the maker_opts.ctl file).
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 1/10/14, 2:48 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
>> wrote:
>> 
>>> Hi Carson and other maker developers,
>>> 
>>> I was reading the source code of the latest maker release and noted
>>> several references to ncRNAs, snoscan and trnascan. Can these be
>>> incorporated into the normal annotation workflow? If so, are there any
>>> instructions available for that?
>>> 
>>> best regards,
>>> Mikael Durling
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
>