[maker-devel] is using est_reads option safe?

[Anurag Priyam]

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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>
>