<div dir="ltr">Hi Carson, thanks for your reply.<div><br><div>Yes, I did the same as you. Here are different outputs for the same annotation file: </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">grep -c -P "\tgene\t" Dato_struct-annot.noseq.gff<br>17688<br>grep -c -P "RNA\t" Dato_struct-annot.noseq.gff<br>17688<br>grep -c -P "mRNA\t" Dato_struct-annot.noseq.gff<br>17205<br>grep -P "RNA\t" Dato_struct-annot.noseq.gff| cut -f3 | sort -u<br>mRNA<br>tRNA</blockquote><div><br></div><div>After using a tool to extract transcripts sequences in a Fasta file, y obtained 17205 sequences. Looking for those genes without an associated transcript, it seems that you can only find tRNAs annotated there. It is odd:</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Backbone_23 maker gene 486041 486112 . - . ID=Dato03103;Name=Dato03103;Alias=trnascan-Backbone_23-noncoding-Glu_CTC-gene-4.38;<br>Backbone_23 maker tRNA 486041 486112 . - . ID=Dato03103-RA;Parent=Dato03103;Name=Dato03103-RA;_AED=1.00;_QI=0|-1|0|0|-1|0|1|73|0;_eAED=1.00;<br>Backbone_23 maker exon 486041 486112 . - . ID=Dato03103-RA:exon:45875;Parent=Dato03103-RA;</blockquote><div><br></div><div> The AED is bad in this example, so I'm thinking that it would be possible this gene had no evidence supporting it. <br>I do not understand either the "Alias" for the gene line, it looks like trnaScan detected the gene.<br></div><div>Any ideas?</div><div><br></div><div><br></div><div>Nicolás</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><i style="font-family:arial,helvetica,sans-serif;font-size:12.8px">--</i></div><div><i style="font-family:arial,helvetica,sans-serif;font-size:12.8px">Nicolas Nahuel Moreyra</i><br></div><div><font face="arial, helvetica, sans-serif"><i>BSc/MSc in Bioinformatics</i></font></div><div><font face="arial, helvetica, sans-serif"><i>CONICET PhD Fellow @ IEGEBA</i></font></div><div><font face="arial, helvetica, sans-serif"><i>PhD Student in Comparative Genomics @ <span style="font-size:12.8px;white-space:pre-wrap">EGE (</span></i></font><i style="font-family:arial,helvetica,sans-serif;font-size:12.8px">FCEyN - UBA) </i><font face="arial, helvetica, sans-serif"><i><span style="font-size:12.8px;white-space:pre-wrap">-> </span></i><span style="white-space:pre-wrap"><i><a href="mailto:nmoreyra@ege.fcen.uba.ar" target="_blank">nmoreyra@ege.fcen.uba.ar</a></i></span></font><span style="font-size:12.8px"> </span></div><div><span style="font-size:12.8px">Professor of Bioinformatics @ Favaloro University</span><br></div><div><span style="font-size:12.8px">Professor of Informatics @ IFTS N° 7</span></div><div><i style="font-family:arial,helvetica,sans-serif"><span style="white-space:pre-wrap;font-size:12.8px">Argentina</span></i><br></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><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El mar., 26 de may. de 2020 a la(s) 14:54, Carson Holt (<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">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="color:rgb(0,0,0)">grep -c -P “RNA\t” file.gff</span>"<br><div><br></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></div><div>Thanks,</div><div>Carson</div><div> </div><div><br><blockquote type="cite"><div>On May 21, 2020, at 7:58 AM, Nicolás Moreyra <<a href="mailto:niconm89@gmail.com" target="_blank">niconm89@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><div>Dear all, </div><div><br></div><div>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>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>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><br>Thanks in advance.<br><br>Nicolás<br></div><br clear="all"><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><i style="font-family:arial,helvetica,sans-serif;font-size:12.8px">--</i></div><div><i style="font-family:arial,helvetica,sans-serif;font-size:12.8px">Nicolas Nahuel Moreyra</i><br></div><div><font face="arial, helvetica, sans-serif"><i>BSc/MSc in Bioinformatics</i></font></div><div><font face="arial, helvetica, sans-serif"><i>CONICET PhD Fellow @ IEGEBA</i></font></div><div><font face="arial, helvetica, sans-serif"><i>PhD Student in Comparative Genomics @ <span style="font-size:12.8px;white-space:pre-wrap">EGE (</span></i></font><i style="font-family:arial,helvetica,sans-serif;font-size:12.8px">FCEyN - UBA) </i><font face="arial, helvetica, sans-serif"><i><span style="font-size:12.8px;white-space:pre-wrap">-> </span></i><span style="white-space:pre-wrap"><i><a href="mailto:nmoreyra@ege.fcen.uba.ar" target="_blank">nmoreyra@ege.fcen.uba.ar</a></i></span></font><span style="font-size:12.8px"> </span></div><div><span style="font-size:12.8px">Professor of Bioinformatics @ Favaloro University</span><br></div><div><span style="font-size:12.8px">Professor of Informatics @ IFTS N° 7</span></div><div><i style="font-family:arial,helvetica,sans-serif"><span style="white-space:pre-wrap;font-size:12.8px">Argentina</span></i><br></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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