Hi everyone,

This post is the second part of a question I already ask and I couldn't find any answers :

https://www.biostars.org/p/206213/#206286

I need a alternative to Cufflinks in order to process the bam files produced by Tophat2.
Indeed, I tried several time to use it, but each time, Cufflinks froze at the exact same location on my canu assembly (tig00000382:15043-15157) , and it can last forever.

My RNAseq data seem to be fine, since a colleague could analyse them (with an other assembly reference to align against with tophat), and use Cufflinks who didn't behave the same way, it didn't froze and do the job.

You can have more information about my problem on an issue I posted on github : https://github.com/cole-trapnell-lab/cufflinks/issues/72

It seems that I'm not the only one you got this problem.

For an alternative, I heard about Trinity, but I don't know that much about it, and about the differences between Trinity and Cufflinks.

Can I have some advices please ?

Thanks for helping !

Cheers,

Roxane
[StringTie][1] is pretty much a complete replacement for Cufflinks for transcript assembly and quantification. Its way faster than Cufflinks (e.g. a recent job that took Cufflinks 40 CPU hours took StringTie 1 CPU hour).

If you want to create your own transcript annotations, I definitely recommend using it. 

For quantitaition, I'd recommend the alignment free algorithms (Kallisto, Salmon etc), as several people's benchmarks have recently shown them to be more accurate than the alignment based methods. See [here][2], [here][3] and [here][4].


  [1]: https://ccb.jhu.edu/software/stringtie/
  [2]: https://cgatoxford.wordpress.com/2016/08/17/why-you-should-stop-using-featurecounts-htseq-or-cufflinks2-and-start-using-kallisto-salmon-or-sailfish
  [3]: http://f1000research.com/slides/4-741
  [4]: http://www.ncbi.nlm.nih.gov/pubmed/26335491