I am new to RNA-seq and am planning on mapping to the transcriptome of Mus Musculus. However, I ran into a few questions. Can either bowtie or HISAT2 be used for mapping onto the transcriptome, or does only bowtie work for this? Also, when creating an index before alignment, instead of inputting the genome, do I just input the cDNA file? Lastly, when doing counts using HTSeq-count, do I input the same GTF file used for that of the genome?
Answering any part of the question would help.
EDIT: As of now, I am only interested in differential gene expression.