<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="">The result.maker.proteins.fasta and result.maker.transcripts.fasta files contain the filtered annotations, and the other files are for reference purposes (i.e. snap and augustus raw unfiltered output). The non_overlapping_ab_initio files contain non-redundant ab initio predictions that do not overlap a final annotation (maker file). They were called by a predictor but rejected for lack of support. If you wanted to look for a potential missing gene model, that is where it would be.<div class=""><br class=""><div class="">—Carson<br class=""><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 23, 2020, at 12:03 AM, <a href="mailto:maker-devel-owner@yandell-lab.org" class="">maker-devel-owner@yandell-lab.org</a> wrote:</div><br class="Apple-interchange-newline"><div class="">As list administrator, your authorization is requested for the<br class="">following mailing list posting:<br class=""><br class=""> List: <a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class=""> From: <a href="mailto:nanshangogo@gmail.com" class="">nanshangogo@gmail.com</a><br class=""> Subject: Qusetion about the ab initio gene predictors result<br class=""> Reason: Post by non-member to a members-only list<br class=""><br class="">At your convenience, visit:<br class=""><br class=""> <a href="http://yandell-lab.org/mailman/admindb/maker-devel_yandell-lab.org" class="">http://yandell-lab.org/mailman/admindb/maker-devel_yandell-lab.org</a><br class=""><br class="">to approve or deny the request.<br class=""><br class=""><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">nanshan yang <<a href="mailto:nanshangogo@gmail.com" class="">nanshangogo@gmail.com</a>><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Qusetion about the ab initio gene predictors result</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">December 23, 2020 at 12:03:35 AM MST<br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class=""></span></div><br class=""><br class=""><div dir="ltr" class=""><span style="font-family: Roboto, RobotoDraft, Helvetica, Arial, sans-serif; font-size: 14px;" class="">Hi MAKER community</span> :<div class="">I have questions about MAKER output files.I get result from <span class=""><i class="">ab initio</i> gene predictors which use snap and augustus by maker,and after </span>fasta_merge step,there are some fasta files as:</div><div class="">result.maker.augustus_masked.proteins.fasta<br class="">
result.maker.augustus_masked.transcripts.fasta<br class="">
result.maker.augustus.proteins.fasta<br class="">
result.maker.augustus.transcripts.fasta<br class="">
result.maker.non_overlapping_ab_initio.proteins.fasta<br class="">
result.maker.non_overlapping_ab_initio.transcripts.fasta</div><div class="">result.maker.snap.proteins.fasta</div><div class="">
result.maker.snap_masked..transcripts.fasta </div><div class=""><div class="">result.maker.snap_masked..proteins.fasta</div><div class="">
result.maker.snap.transcripts.fasta </div>
result.maker.proteins.fasta<br class="">
result.maker.transcripts.fasta<br class=""></div><div class="">if i continue to analysis the fasta files,which fasta should i choose?</div><div class="">because i choose <i class="">ab initio</i> gene predictors,so the
result
.maker.non_overlapping_ab_initio*fasta can be uesed into the downstream analysis？or the
result.maker.proteins.fasta
</div><div class="">Thanks verymuch for any help or insights<br class=""></div></div>
<br class=""><br class=""><br class=""><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:maker-devel-request@yandell-lab.org" class="">maker-devel-request@yandell-lab.org</a><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">confirm 102e4151023f6d0466a7c780132e8ca169e86aaa</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">December 23, 2020 at 12:03:58 AM MST<br class=""></span></div><br class=""><br class="">If you reply to this message, keeping the Subject: header intact,<br class="">Mailman will discard the held message. Do this if the message is<br class="">spam. If you reply to this message and include an Approved: header<br class="">with the list password in it, the message will be approved for posting<br class="">to the list. The Approved: header can also appear in the first line<br class="">of the body of the reply.<br class=""><br class=""></div></blockquote></div><br class=""></div></div></body></html>