[maker-devel] is using est_reads option safe?

[Carson Holt]

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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