Sequences of isoforms of a gene from RNAseq data

Question

[mfahim]

I have finished pair-end RNAseq analysis using Tuxedo Protocol. Now I need to extract sequences of different isoforms of a gene from my samples (a total of 6).

How should I proceed?

I guess I have to use *.bam, *.gtf files but how?

I tried GenomicFeatures in R but it gets complicated for Arabidopsis and the commands are not so straightforward. If you have done something similar using GenomicFeatures then I would appreciate if you can send me your script otherwise,

Something java-based on web-based would be great. I don't have full command over command-prompt/python etc.

Cheers