I have some RNA-Seq files which include such data:

Tag    CopyNumber    TPM(Transcript Per Million)
CATGAAGCTAACCCTGAAGGC    2    0.30
CATGGTGGAGTAGATGCTAGT    2    0.30
CATGCTCCACCCGGAAAAAAA    2    0.30
CATGCTCACACTCACTTCTCA    2    0.30
CATGTTATTCAGACATTACAT    2    0.30
CATGGGCTTCCAGTTGAATTT    2    0.30

I wanna make a gene level expression matrix, I am sure I can do it using Bioconductor packages but I do not know which packages can be helpful. There is a package, named "ShortRead", I think it is useful but I do not know how use it for my data.

I appreciated it if anyone could help.