Aligning reads to custom plasmid sequence

Hello everyone,

I have RNA-Seq data from mouse cells which are transfected with a plasmid. I would like to check whether or not I have reads aligning to this plasmid-sequence in my samples.
What would be a smart way to tackle this question? I know there is an option to generate your own genome in STAR after adding the sequences to a fasta file. But I think this option is not available on galaxy. Is there a better way?


If you have the sequence of the plasmid in FASTA you an upload this sequence and align your reads against this FASTA file.


  1. Bowtie2: align the reads to the mouse reference genome; extracted unaligned genes
  2. Upload the plasmid sequence fasta into Galaxy
  3. Normalize it!
  4. Align the unaligned reads from Bowtie.