How do I check splice isoforms for a single gene of interest starting with FASTQ files as input?

Thanks.

You can use Salmon to quantify isoform expression, if you know that the isoforms of interest are contained in the gene annotation. You can check this by first aligning the reads to the genome using a spliced aligner like STAR or HISAT, and then comparing the spliced reads to the reference with a visualization tool like IGV.

Once you've quantified with Salmon, you could load these isoform quantifications into R with:

txi <- tximport(files, type="Salmon", txOut=TRUE)

Then I would start with simple plots of the TPM for the different isoforms of interest across samples. The TPM are stored in txi$abundance.