<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi John,</div><div class=""><br class=""></div>Do you mean the match/match_part features that are source snap_masked? Those are not genes, they are reference alignments representing the ab initio SNAP calls, and it would be incorrect to rename them. They do not have a 1 to 1 relationship with the final gene models. Sometimes a gene model will overlap 2 or more uninformed SNAP ab initio reference alignments, or one SNAP reference alignment may overlap multiple final gene models, so names cannot just be passed from one to the other.<div class=""><br class=""></div><div class="">If you want to add specific SNAP models to the final annotation set, you would need to upgrade them to being a gene/mRNA/exon/CDS feature before you can do that. You can do that with manual editors like Apollo, or you can supply a subset of the features you want to upgrade to maker in the pred_gff= option as a separate run, put existing models in model_gff=, and run with keep_preds=1.</div><div class=""><br class=""></div><div class="">I know I have covered this previously in greater detail as part of the devel list. If you search the archives for the keywords pred_gff, keep_preds, and iprscan you should come across a number of threads that may be helpful —> <a href="https://groups.google.com/forum/#!forum/maker-devel" class="">https://groups.google.com/forum/#!forum/maker-devel</a> </div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 22, 2016, at 2:38 PM, John Cornelius <<a href="mailto:jcornel3@asu.edu" class="">jcornel3@asu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi, I'm using the maker_map_ids script to change the gene ids on an annotation that I just finished. However, I noticed that it does not change the name of genes predicted by SNAP. Is there any way to include SNAP genes for consideration by maker_map_ids? Thanks.<br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class="">John Cornelius<br class="">MCB PhD Candidate<br class="">Arizona State University<br class=""></div></div>
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