Denovo transcript assembly with data from different library types.

Question

[GouthamAtla]

Hi All,

Are there any de novo transcript assembly tools that simultaneously considers different types of libraries ( fr-first strand + fr-stranded etc ) to assemble transcripts ? I know a tool GRIT developed in Ben Browns lab that integrates different data types to get but it requires more specific data sets.

I have stranded RNa-Seq and PE-CAGE ( fr-firststrand ).

Sorry if its a naive question. It's been a while I have not looked into transcript assembly tools.

[Matteo Schiavinato]

Take a look at StringTie.

It doesn't work simultaneously with different library types but it can handle them very well and you might combine the data afterwards.

[GouthamAtla]

I am looking for something that use both the data sets simultaneously. Otherwise, I would not achieve the best transcript models.

[Medhat]

I think SOAPdenovo-Trans could do what you need, also trans-abyss (the Abyss genomic version accept multi lib)

[Asaf]

I think rnaSPAdes should deal with these library types simultaneously.