Looking for the sequence of a particular transcript from sequencing data

[the_august]

First, let me tell you that I'm very new to the field of NGS and not much familiar with the set of tools commonly used for NGS data processing. However, I'm not new to Bioinformatics, and have quite some experience in Linux, Python, Perl , R etc.

I've to find out the sequence of a particular transcript from a set of mouse fastq files. I've extracted the sequence reads for this particular sequence using bbduk.sh of the bbmap package using the following command:

bbduk.sh  in=/me/clumpedSRA.fq.gz ref=/me/known_transcript.fasta k=13 outm=/me/knownT_reads_only.fastq

Can somebody tell me how to get the sequence of the transcript from this reads of the sequence of interest? Can any other tools from 'bbmap' be used?

Besides, I've access to Tophat and Trinity on a high performance cluster.

Thanks in advance