[maker-devel] is using est_reads option safe?

[Carson Holt]

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