Including plasmid in alignment

Question

[heelpPlease]

Hi there

I want to look at differential expression in a bacterial strain. I want to use both STAR and BOWTIE2 for alignment to check out which one works better. It is important that the plasmid is included in the analysis. Would it be ok to just add the plasmid to the genome? Or are there better ways? Thank you!

Answer 1

[GenoMax]

I want to use both STAR and BOWTIE2 for assembly

Those programs are aligners not assemblers. But since you are working with bacteria you likely don't need to do any assembly. Any aligner will work for bacteria since you don't need to worry about splicing.

Yes you can add the plasmids as extra "chromosome" in the genome file, if you are interested in transcripts from those.