paired-read transcriptome data analysis

[joseph]

Can someone point out programs or algorithms to process Illumina sequencing data? I have human paired-read transcriptome data in the form s_N_R_export.txt (the results of alignment of all reads in the lane); I would like to study the mappability of the reads to the human genome, examine splicing and alternative splicing, determine the gene expression levels and ultimately the differential gene expression.
Thanks
Joseph

[ECO]

Hey there... Head over to the Bioinformatics forum, there are many answers to your question!