[maker-devel] is using est_reads option safe?

[Anurag Priyam]

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
>>>>
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>>>
>>>
>
>