Hello! I ran Maker on a chromosome-level mollusc genome using some evidence I previously generated with Funannotate and BRAKER2, but Maker is not

to set est_forward=1 in the control files during the maker run (must manually add it). It is a hack for fast protein mapping of previous annotations onto new assemblies. But you can use

recovery when est_forward=1 is set). You can compare neighboring genes between assemblies to see if one copy is simply a paralog. If there are a lot of genes with 2 copies, you probably

add > est_forward=1 to the maker_opts.ctl file names will be copied from the > alignment source and the score in the GFF3 column will be the percent match > to the original transcript

you add est_forward=1 the score column in the GFF3 will be the % match to the original model. It's and easy way to select only models with a very high percent match. Remove models without

using the est_forward=1 #reserve flag for map2assembly option to transfer a transcriptome to the genome and create directly gene models from it. This usually works ok but on a larger

devel/est_forward%7Csort:date/maker-devel/gDbvTknuep4/gDiGCMgjCQAJ >> >> This will help map old structural models to new coordinates. Moving >> functional

and undocumented est_forward=1 option, it will override a number of internal values. —Carson From: David Hughes > Subject: MAKER v3.0.0. Date: October 23, 2019 at 8:24:24 AM MDT

this option est_forward=1 (won't already be there). It's not perfect but it will produce a GFF3 with gene models based entirely on alignment of the old models. You can then

also set est_forward=1 to get the names from the old models (you have to add it as it's not already there). If you want to try and force an alignment to a specifc location, you can also

to add est_forward=1 to the control files to have MAKER try and > >>>> derive model names from the name of evidence alignments they were > >>>> derived

with setting est_forward=1. But in output I'm getting large number of genes. My input cDNA fasta contains ~35K genes and after mapping there are ~58K genes. I'm using maker

I've attached a protocols paper that walks through what you are trying to do. Let me know if it helps. Mike > On May 12, 2016, at 8:37 PM,

Hi Florian, Your not off topic here. I've attached the paper. Looking at the plot you sent I'm guessing that there is red dot right underneath

> > est_forward=1 > > > > After run Maker, some genes were lost. There are 14146 transcritpts as input. Only 13092 gene models were in the output. Anyone know the reason

. The est_forward tool used to pull IDs forward is based solely off of alignment (they will not all be exact matches or complete matches - just best matches), so you cannot guarantee that

> CTL_OPTIONS est_forward 0 > CTL_OPTIONS correct_est_fusion 0 > CTL_OPTIONS alt_splice 0 > CTL_OPTIONS always_complete 0 > CTL_OPTIONS alt_peptide C > CTL_OPTIONS

Hi, I compiled all annotations generated by MAKER into a single GFF file using the gff3_merge script

Is it possible to migrate annotations from an old assembly to a new assembly using MAKER? Perhaps by

control file est_forward=1. This is normally used to move transcripts forward onto new assemblies with names being drawn from the alignment, but by telling MAKER that these are ESTs

Hi, I'm annotating a genome using a closely related genome from Genbank, using the .frn (RNA) and

devel] est_forward and conflicting names Interesting. Thanks for the clarification. I'm working on a plant mitochondrion, and so as far as I know, there's no alternative

Behavior Options est_forward=1 #map names and attributes forward from EST evidence, 1 = yes, 0 = no single_exon=1 #consider single exon EST evidence when generating annotations

Hi, we are assembling and annotating genomes for several related strains of Caenorhabditis worms and

Hi, in a previous thread, the maker_coor feature for ETSs was mentioned. I have been trying it out,

Hi all I'm looking to move existing transcripts from one genome assembly to another, keeping the

Hi all, I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta.

Hello, I have run maker 2.03 on a genome that we assembled a while back. Now we have a new genome

file. est_forward=1 This is sort of a quirky way to cause MAKER to run the same as map2assembly (They are basically the same programs under the hood). Scan the output GFF3 to see if any

0 CTL_OPTIONS est_forward 0 CTL_OPTIONS alt_splice 0 CTL_OPTIONS always_complete 0 CTL_OPTIONS alt_peptide C CTL_OPTIONS evaluate 0 CTL_OPTIONS blast_type ncbi CTL_OPTIONS