[maker-devel] different number of annotated genes and transcripts

[Carson Holt]

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 “grep -c -P “RNA\t” file.gff"

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).

Thanks,
Carson
 

> On May 21, 2020, at 7:58 AM, Nicolás Moreyra <niconm89 at gmail.com> wrote:
> 
> Dear all, 
> 
> First of all, thank you for sharing your experiences here. I tried to find this issue in the posts already made but failed.
> 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.
> 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? 
> 
> Thanks in advance.
> 
> Nicolás
> 
> --
> Nicolas Nahuel Moreyra
> BSc/MSc in Bioinformatics
> CONICET PhD Fellow @ IEGEBA
> PhD Student in Comparative Genomics @ EGE (FCEyN - UBA) -> nmoreyra at ege.fcen.uba.ar <mailto:nmoreyra at ege.fcen.uba.ar> 
> Professor of Bioinformatics @ Favaloro University
> Professor of Informatics @ IFTS N° 7
> Argentina
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