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gene-annotation.adoc

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Reference gene annotation

Look at the mouse gene annotation (ensembl v65, long genes):

more ~ngs00/refs/mm65.long.ok.gtf

Type q to exit the view.

Store information about gene Sec23a in a separate file:

grep Sec23a ~ngs00/refs/mm65.long.ok.gtf > Sec23a.gff

Count the number of transcripts of this gene:

awk '$3=="transcript"' Sec23a.gff | wc -l

Count the number of exons of this gene:

awk '$3=="exon"' Sec23a.gff | wc -l

What is the biotype of the gene?

What is the biotype of each transcript of this gene?