Re: [maker-devel] How do I extract matrix from annotation

[Carson Holt]

This is an older email that looks like never got an answer. Briefly you need to use Linux command line tools to evaluate the GFF3 file.

Examples:

#count protein coding transcripts

cat annotations.gff | grep -c -P “\tmRNA\t"

#count tRNA transcripts

cat annotations.gff | grep -c -P “\ttRNA\t"

#count snoRNA transcripts

cat annotations.gff | grep -c -P “\tsnoRNA\t"

You can also pull out the Parent feature and count uniq entries to look at genes instead of transcripts. Example:

#count protein coding genes

cat annotations.gff | grep -c -P “\tmRNA\t” | perl -ane ‘/Parent=([^\;\n]+)/; print "$1\n”’ | sort | uniq | grep -c “"

You can also try tools like SOBA from the Sequence Ontology that give statistics on GFF3 features —> http://www.sequenceontology.org/cgi-bin/soba.cgi

—Carson

On Jul 27, 2021, at 9:15 AM, Emmanuel Nnadi <een...@gmail.com> wrote:

Hello Carson, Greetings from Nigeria.

Please how can I extract these matrix from my annotations?

Number of  protein-coding genes in the assembled tea plant genome  Those with known proteins and/or domains . Annotation of noncoding RNA genes  ribosomal RNA genes Number of  transfer RNA genes, Number  transcription factor genes and  simple sequence 

Thanks

Nnaemeka Emmanuel Nnadi,Ph.D

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

+2348068124819

Publications: 

https://orcid.org/0000-0002-8424-4859

 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications