Here, you need to find the number of reads that are mapped to the given transcripts. For this purpose you need mapped BAM file, the transcript chromosome number and it's start-end co-ordinates. If you have this information, you can find read coverage using samtools as follows

samtools view BAM_file Chromosome:start-end

It will give you all reads that mapped to given transcript region. To count the read coverage, you can pipe wc -l command

samtools view BAM_file Chromosome:start-end | wc -l

Alongside samtools, bedtools offers ways of reading Tophat/cufflinks output too http://bedtools.readthedocs.io/en/latest/index.html

In addition to the tools mentioned earlier, commonly used tools for counting reads in a genomic interval (gene, exon,...) are featureCounts and htseq-counts. I would recommend featureCounts, because it's very fast, has convenient options, but htseq-counts also works fine. Both are nicely documented.