Obtain fragments from RNA-Seq reads?

Question

[tmms]

Hello

If have RNA-Seq data (paired end reads) of samples of human tissue. Is it possible to reconstruct the fragments (parts of cDNA that got sequenced) with that data? If so, how is a good way to do that?

I already looked on the internet, but most mappers I could find align the human genome.

Thanks in advance.

[Antonio R. Franco]

I don't understand what you are asking.. Can you clarify your question ?

[tmms]

I have two files with paired end reads from RNA-Seq. I do not know the insert size. I want to obtain the sequence of the fragments (molecules that were sequenced) if possible.

[GenoMax]

Did you miss finding Trinity?

[tmms]

Thanks for the suggestion. I did not find that one.

[Nicolas Rosewick]

You could align on the transcriptome, extract alignement position officielle R1 and R2 and then extract the relative sequence from the transcript using bedtools