<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="">Cufflinks2gff is not a general GTF to GFF3 converter. It will work with cufflinks, but I don’t think it will convert Stringtie. Also if you are trying to use est2genome=1, it only works with fasta files.<div class=""><div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 29, 2018, at 8:24 PM, <a href="mailto:ytshen@genetics.ac.cn" class="">ytshen@genetics.ac.cn</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class=""></span>Dears,</div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">I am trying to run MAKER for a plant genome and want to use RNA-seq information for my annotation. <span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">For this purpose, I alignment RNA-seq reads to my genome by using Hisat2 and assemble transcripts by using Stringtie, and transfer the </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">Stringtie </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""><b class="">gtf</b><span class="Apple-converted-space"> </span>output file into<span class="Apple-converted-space"> </span><b class="">gff</b><span class="Apple-converted-space"> </span>file by using Cufflinks2gff script provided by MAKER (ver 2.31.10).</span></div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> When I set the gff file as<b class=""> est_gff</b> in </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">maker_opts.ctl file, </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">the MAKER running will stop at some point, but<b class=""><span class="Apple-converted-space"> </span>it didn't provide any error or warning information and also didn't exist</b>. But when I transfer the gff file into fasta file, and set it as est_fasta </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">in </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">maker_opts.ctl file, </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">the MAKER can run successfully.</span></div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">Has this phenomenon happened to someone else? How I can fix it? Hope your reply!</span></div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Thank you very much!</div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Best!</div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Sinceraly,</div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Yanting</div><div style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><hr size="1" align="left" style="caret-color: rgb(0, 0, 0); font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; 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