Dose Cufflinks work on bacterial RNA-seq ?

[James_yang]

Dear all,

I am a new one who getting start in RNA-seq area.

I have read the Cufflinks's paper and known it's a reference base assembler.

And Now, I have two dataset.
1. a bacterial genome assembled by Ray (denovo assembly)
2. 3 condition of this bacteria of RNA-seq.

I am wondering can I use the denovo-genome as a reference and use predicted ORF (from genome) as guild-transcript to run Cufflinks?

Dose the process get any problem?

Thanks a lot
James

[peskador]

Dear James,

I hope that I can help you!

I don't recommend Cufflinks for bacterial rna-seq tech, you can use it... And in fact it works pretty well.

There are other programs that you can check out like EDGE-Pro and Rockhopper. Actually I recommend that you use all of them and compare the results..

I haven't worked with de novo assembly, but I think you can use ray output to use as your reference genome... Other people here can help you further