<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">MAKER requires the two level match/match_part format. An example of which can be found in the GFF3 specification —> <a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md" class="">https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md</a><div class=""><br class=""></div><div class="">I haven’t used PASA, but the file you are providing may be GFF2 or GTF format which is not compatible with GFF3.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 9, 2018, at 9:15 AM, Federico López <<a href="mailto:flopezo84@gmail.com" class="">flopezo84@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello,<div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""></div></div></div></div></div></div>
<div class=""><br class=""></div><div class="">I was wondering what might be the recommended option for using PASA2 alignment assemblies with MAKER3:</div><div class=""><br class=""></div><div class=""><div class="">1. PASA assemblies in FASTA format (est)</div><div class="">2. PASA assembly structures (est_gff)</div><div class="">3. ORFs from PASA assemblies (protein)</div></div><div class=""><br class=""></div><div class="">And related to this question, when I use the PASA2 assembly structures in GFF3 format, MAKER reports the error below.</div><div class=""><br class=""></div><div class="">"ERROR: Non-unique top level ID for..."<br class=""></div><div class=""><br class=""></div><div class="">I suppose all the non-unique IDs need to be renamed for MAKER?</div><div class=""><br class=""></div><div class="">Any help is greatly appreciated.</div></div>
_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></body></html>