[maker-devel] is using est_reads option safe?

[Anurag Priyam]

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