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<div><span></span>Dears,</div><div><br></div><div>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;">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;">Stringtie </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;"><b>gtf</b> output file into <b>gff</b> file by using Cufflinks2gff script provided by MAKER (ver 2.31.10).</span></div><div><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;"><br></span></div><div><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;"> When I set the gff file as<b> est_gff</b> in </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">maker_opts.ctl file, </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">the MAKER running will stop at some point, but<b> 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;">in </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">maker_opts.ctl file, </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">the MAKER can run successfully.</span></div><div><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;"><br></span></div><div><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">Has this phenomenon happened to someone else? How I can fix it? Hope your reply!</span></div><div><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;"><br></span></div><div>Thank you very much!</div><div><br></div><div>Best!</div><div><br></div><div>Sinceraly,</div><div>Yanting</div>
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