Obtain fragments from RNA-Seq reads?
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.
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Nicolas Rosewick
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tmms •
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I don't understand what you are asking.. Can you clarify your question ?
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.
Did you miss finding Trinity?
Thanks for the suggestion. I did not find that one.
You could align on the transcriptome, extract alignement position officielle R1 and R2 and then extract the relative sequence from the transcript using bedtools