I want to map a set of sequences (derived from RNA) against a bacterial
genome. Unfortunately, the genome of Synechococcus sp. PCC 7002 consists
of one chromosome and six plasmids. In MAQ I can chose only one DNA
entry for mapping. In local BLAST it was possible to generate databases
consisting of several DNA entries to map the data.
Does anybody have experience in mapping transcription data against
complex genomes in Galaxy.