This is a test version of Biostars. For the public version, visit https://www.biostars.org.
bacterial genome annotation for rna seq analysis

Dear all,

I have performed transcriptomic experiment for 3 bacterial strains. I have the the complete sequence genome of these strains that are homogeneous except some few SNPs between their genomes. One of these genome is annotated and I want to annotate the two others in order to conserve the same name of the genes for RNA-seq analysis. If you have a methodology suggestion I''ll be thankful.

genome annotation gene
• 2,528 views • link
updated by thackl thackl • written by slimane.khayi • slimane.khayi

1 answer

MAKER's map2assembly might be able to do what you want. However, installing maker might be a bit over the top...

Usage:
     map2assembly <genome.fasta> <transcripts.fasta>
     Maps old gene models to a new assembly where possible.
• 0 views • link
written by thackl thackl

Log in to answer this question.

More posts like this