I am new to QuasR and trying to analyse RNASeq data of Tomato plant, whose genome has not been included in the package. Kindly guide me as to how to proceed with the transcriptome analysis of organisms not included here.
It's no problem to use QuasR for an organism for which there is no BSgenome package available.
In that case, you can use a genome reference in the form of a fasta file (see for example the code in section 3.2 of the vignette, or also the documentation in ?qAlign). In your qAlign call, you then refer to that fasta file, e.g. for RNA-seq data you could:
and you can also use the clObj argument to enable parallel processing.
An alignment index for the genome will automatically created in the same folder containing genome.fa, so make sure you have write permission to that folder.