<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Masa,<div><br></div><div>Also, if you want additional SNAP output that hasn't been passed forward in MAKER you can alway access the original SNAP output files in the MAKER datastore. This is a directory structure created by MAKER to store contig specific data. There is a datastore directory (and a corresponding index file) in the make output directory. The index file will provide the path to individual contigs and in that contig specific directory there is a directory call theVoid. This contains all of the output of each program that MAKER runs.<div><br></div><div>B</div><div><br><div><div>On Feb 13, 2014, at 1:11 PM, Carson Holt wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>No. Snap genes do not disappear. All SNAP ab initio calls will always be<br>kept as reference fetters marked snap_masked (for repeat masked genome)<br>and snap (for unmasked genome). MAKER then runs SNAP another time where<br>it feeds hints to SNAP based on EST and protein alignment evidence. These<br>hint based models can then compete against the ab initio SNAP models to be<br>promoted to genes if their AED scores are better. Fianl models can also<br>get UTR added based on EST evidence. That is why you can get models from<br>MAKER that do not match the original SNAP ab initio calls.<br><br>So in summary, all SNAP ab initio models will be in snap_masked. The<br>MAKER models will consist of hint based SNAP rerun plus SNAP ab intio<br>models processed to add UTR.<br><br>Thanks,<br>Carson<br><br><br><br>On 2/13/14, 3:17 AM, "Masa Roller" <<a href="mailto:masa@bioinfo.hr">masa@bioinfo.hr</a>> wrote:<br><br><blockquote type="cite">Dear all,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I ran snap2 based gene prediction through maker.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">In the resulting gff file, in the source "snap_masked" I can find the<br></blockquote><blockquote type="cite">score in the score column of every snap prediction that did not get<br></blockquote><blockquote type="cite">promoted to a maker gene. This would be the score of how well the<br></blockquote><blockquote type="cite">prediction matches the HMM?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">It seems to me that those snap models that are given gene status no<br></blockquote><blockquote type="cite">longer appear as snap_masked source but only as source "maker". Maker<br></blockquote><blockquote type="cite">then removes the score column, instead giving AED and eAED scores (which<br></blockquote><blockquote type="cite">are more about how the model corresponds to the evidence). When viewing<br></blockquote><blockquote type="cite">the maker transcripts and SNAP predictions in a browser, they do not<br></blockquote><blockquote type="cite">match (mostly, maker predictions are longer).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am interested in the score of individual gene predictions that<br></blockquote><blockquote type="cite">underlined maker gene models. Where could I find that information?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Many thanks!<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">maker-devel mailing list<br></blockquote><blockquote type="cite"><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br></blockquote><blockquote type="cite"><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><br></blockquote><br><br><br>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div></span><br class="Apple-interchange-newline">
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