recently I have been trying to get some information regarding the gene structure of a few mouse genes. All I have is an RNA-Seq-derived SRA raw file. I used it to generate a FASTQ file using fastq-dump from SRA Toolkit. I then run tophat from TopHat2/Bowtie2 to align FASTQ reads to genomic reference. Unfortunately tophat turned out to be extremely slow on the machine I am using. However, since what I actually need is just to check a few loci, I would like to know if there are alternative solutions. For example, could I use single FASTA files (retrieved from Ensembl for each locus) to generate small, locus-specific indexes?