<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="">Perhaps you are counting wrong. If you want to know the number go genes, you must look at the GFF3. You can use ‘grep -c -P “\tgene\t” file.gff’, then the number of transcripts would be “<span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">grep -c -P “RNA\t” file.gff</span>"<br class=""><div><br class=""></div><div>Note that if you are using things like tRNAscan, you will get tRNA transcripts and associated genes. If you are trying to count from the fasta files, make sure you use the right file (maker.proteins.fasta and maker.transcripts.fasta).</div><div><br class=""></div><div>Thanks,</div><div>Carson</div><div> </div><div><br class=""><blockquote type="cite" class=""><div class="">On May 21, 2020, at 7:58 AM, Nicolás Moreyra <<a href="mailto:niconm89@gmail.com" class="">niconm89@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Dear all, </div><div class=""><br class=""></div><div class="">First of all, thank you for sharing your experiences here. I tried to find this issue in the posts already made but failed.</div><div class="">Secondly, I am sorry for asking you a silly question (I think), but after I complete the genome annotation of four species, I obtained fewer transcripts than genes. I do not understand why MAKER annotated genes unable to transcribe.</div><div class="">I was trying to find the reason for this issue to discuss it in my thesis but I am a bit lost. Has this happened to anyone? Is there any possible cause that comes to mind? <br class=""><br class="">Thanks in advance.<br class=""><br class="">Nicolás<br class=""></div><br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><i style="font-family:arial,helvetica,sans-serif;font-size:12.8px" class="">--</i></div><div class=""><i style="font-family:arial,helvetica,sans-serif;font-size:12.8px" class="">Nicolas Nahuel Moreyra</i><br class=""></div><div class=""><font face="arial, helvetica, sans-serif" class=""><i class="">BSc/MSc in Bioinformatics</i></font></div><div class=""><font face="arial, helvetica, sans-serif" class=""><i class="">CONICET PhD Fellow @ IEGEBA</i></font></div><div class=""><font face="arial, helvetica, sans-serif" class=""><i class="">PhD Student in Comparative Genomics @ <span style="font-size:12.8px;white-space:pre-wrap" class="">EGE (</span></i></font><i style="font-family:arial,helvetica,sans-serif;font-size:12.8px" class="">FCEyN - UBA) </i><font face="arial, helvetica, sans-serif" class=""><i class=""><span style="font-size:12.8px;white-space:pre-wrap" class="">-> </span></i><span style="white-space:pre-wrap" class=""><i class=""><a href="mailto:nmoreyra@ege.fcen.uba.ar" target="_blank" class="">nmoreyra@ege.fcen.uba.ar</a></i></span></font><span style="font-size:12.8px" class=""> </span></div><div class=""><span style="font-size:12.8px" class="">Professor of Bioinformatics @ Favaloro University</span><br class=""></div><div class=""><span style="font-size:12.8px" class="">Professor of Informatics @ IFTS N° 7</span></div><div class=""><i style="font-family:arial,helvetica,sans-serif" class=""><span style="white-space:pre-wrap;font-size:12.8px" class="">Argentina</span></i><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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