<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>The map_forward option requires that the pass option for the gene models be turned on. Otherwise you will have to do some spacial overlap test outside of MAKER.</div><div><br></div><div>If you have a new assembly, you can try mapping the old models onto the new assembly using the old transcripts as input to the est= and setting est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is an undocumented option that is still a little buggy (hence why it is still undocumented). Add the line est_forward=1 to your control files. This tells MAKER to copy names from the ESTs, build the models directly from their alignment, and to do other things to try and make a 1 to 1 match across the genome. You will have to manually check that it is 1 to 1 in the end (as I said still a little buggy and hence undocumented). Use the resulting file as input to the model_gff option on a separate run with map_forward=1 for additional reannotation wil more evidence, etc. where you want to still be able to map names forward. </div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Jeremy Semeiks <<a href="mailto:jeremy.semeiks@utsw.edu">jeremy.semeiks@utsw.edu</a>><br><span style="font-weight:bold">Date: </span> Sunday, 9 September, 2012 3:49 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] How to preserve human-friendly IDs when reannotating<br></div><div><br></div>Hi all,<br><br>I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta. The entire project is pretty iterative, in the sense that I first get some seemingly-sane annotation sets, then analyze and compare the proteomes biologically, then reannotate when new data comes in or as I learn more about how maker works. Because I have already attached biological meaning to some of my proteins, I would like to retain the same human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new proteins on a reannotation run because I turned on keep_preds, then I don't want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I run maker_map_ids; I want to keep it named mymold_09652T0.<br><br>So, is there any built-in way to preserve human-friendly IDs, or do I need to write my own script for this? I have tried setting map_forward=1 and maker_gff=<the GFF file output by the previous run of maker_map_ids>, but setting these seems to preserve neither the human-friendly IDs nor even the original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; would this be relevant?<br><br>Extra credit question: I am making some mate-pair libraries for these fungi; when I re-assemble, that will completely change my scaffold names. Is there any easy way to preserve human-friendly transcript names in this case? As with the above simpler case, I think it would be pretty easy to transfer 90% of the names just by doing an all-vs-all blastp between two annotation sets and fishing out the best hits, but the remaining 10% might be a headache.<br><br>Thanks,<br>Jeremy<br>Grad student, Grishin lab<br>UT Southwestern, Dallas TX<br>510.385.8959<br>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>