[maker-devel] is using est_reads option safe?

[Anurag Priyam]

That answers all my questions. Thanks, Carson.

-- Priyam

On Thu, Apr 24, 2014 at 7:45 PM, Carson Holt <carsonhh at gmail.com> wrote:
> It will use both.  you can also provide multiple files to either using
> comma separated lists.
>
> --Carson
>
>
> On 4/24/14, 1:28 AM, "Anurag Priyam" <a.priyam at qmul.ac.uk> wrote:
>
>>You say est_gff is the equivalent of est= (except that alignment
>>structure is a part of gff). What would MAKER do if I set both est=
>>and est_gff= options in maker_opts.ctl? Will it ignore est=?
>>
>>-- Priyam
>>
>>On Wed, Apr 23, 2014 at 8:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>> est_gff is the equivalent of est=, but because the alignment structure
>>>is
>>> already in the GFF3, I don't need to align sequence with
>>>blastn/exonerate.
>>>  model_gff and pred_gff are essentially the same with the difference
>>>being
>>> that model_gff can be kept in the final results even without supporting
>>> evidence, but pred_gff won't.  Pred_gff needs evidence support because
>>>it
>>> is a potential model, where model_gff is considered a known model even
>>>if
>>> the structure of that model may be uncertain.
>>>
>>> other_gff is just a convenience method for passing through GFF3 features
>>> to the final result.  It's impossible to have MAKER be aware of every
>>>kind
>>> of possible entry, so if you have something more exotic in the final
>>> output (sequence variant information, alternate alleles, promotor and
>>> methylation site, etc.) then you can pass it in there and it will just
>>>be
>>> printed into the file.  It's basically the equivalent of concatenating
>>>two
>>> GFF3 files together, but it handles the proper reordering of sequence
>>> information at the end of the GFF3 file (because technically you can't
>>> just concatenate GFF3 files end-to-end).  You can also use the
>>>gff3_merge
>>> tool that comes with MAKER to get the same effect.
>>>
>>> --Carson
>>>
>>>
>>>
>>> On 4/23/14, 3:55 AM, "Anurag Priyam" <a.priyam at qmul.ac.uk> wrote:
>>>
>>>>Thanks, Carson.
>>>>
>>>>I now understand that I shouldn't use est_reds options.
>>>>
>>>>Does MAKER utilise est_gff for prediction or simply passes the
>>>>annotations through to the output GFF? In that case how is it
>>>>different from using other_gff / model_gff (what's the difference
>>>>between these two?)
>>>>
>>>>I have both assembled and raw reads. Is it sufficient to just use the
>>>>assembled set?
>>>>
>>>>-- Priyam
>>>>
>>>>On Tue, Apr 22, 2014 at 11:32 PM, Carson Holt <carsonhh at gmail.com>
>>>>wrote:
>>>>> The est_reads option doesn't do anything.  It in the run log for
>>>>>backwards
>>>>> compatibility with old jobs because MAKER has a restart capability
>>>>>(i.e.
>>>>> people can rerun new MAKER versions against old MAKER output in the
>>>>>same
>>>>> directory - it can reuse old raw results to avoid rerunning analysis
>>>>> steps).  The est_reads was originally there for developer
>>>>>experimentation,
>>>>> but then it went away.
>>>>>
>>>>> You need to use an external tool like tophat and cufflinks to align
>>>>>short
>>>>> reads and assemble them into likely exon blocks (i.e. the GFF3
>>>>>passthrough
>>>>> option you mentioned).  Or you can assemble then without alignment
>>>>>using
>>>>> something like trinity (then you can provide that result to the est=
>>>>> options because it will be in fasta format).
>>>>>
>>>>> You should not use raw reads directly with MAKER, you need to
>>>>>preprocess
>>>>> them using one of the methods mentioned for them to be useful.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> On 4/22/14, 11:45 AM, "Anurag Priyam" <a.priyam at qmul.ac.uk> wrote:
>>>>>
>>>>>>Hi,
>>>>>>
>>>>>>I need to run MAKER against a genome with both raw (FASTQ) and
>>>>>>assembled (FASTA) RNA-Seq data. I point MAKER to assembled data using
>>>>>>est= options in maker_opts.ctl. Looking for how to point MAKER to the
>>>>>>raw reads I came across this thread
>>>>>>https://groups.google.com/forum/#!topic/maker-devel/oLEXJ4z4fDY where
>>>>>>Dr. Carlson Holt points out that est_gff should be used. However, from
>>>>>>MAKER's run log it seems that est_reads option is not deprecated, just
>>>>>>hidden from plain sight by excluding it from maker_opts.ctl. So I set
>>>>>>est_reads option in maker_opts.ctl and MAKER parses the control files
>>>>>>and runs just fine.
>>>>>>
>>>>>>Now I am left wondering if it's safe to use est_reads. As in, could it
>>>>>>impact the predicted set negatively?
>>>>>>
>>>>>>-- Priyam
>>>>>>
>>>>>>_______________________________________________
>>>>>>maker-devel mailing list
>>>>>>maker-devel at box290.bluehost.com
>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>>g
>>>>>
>>>>>
>>>
>>>
>
>