RNA-seq: ab initio reconstruction of transcriptome with prokaryotes

[pasta]

Dear all,

A few programs/pipeline allow ab initio reconstruction of eukaryotic transcriptomes, such as Cufflinks or Scripture.
Do you know any software that would do the same on a RNA-seq dataset from a bacteria (reference sequence available) ? Can I use Cufflinks or Scripture for that purpose?

Many thanks

toni

[goshng]

Hi,

I had the same question. And, I am wondering if anyone answered to this question.

Thanks,

SangChul

[pasta]

Hi Sang,

As you do not have any intron/exon with bacteria, I simply used Velvet and/or Edena for this purpose. Works pretty well.


toni

[son_nexg]

Has anyone tried Cufflink for de novo assembly of bacterial transcript ? If yes, I would be interested in knowing how it went and results obtained

Does anyone have an idea about coverage/depth required for differential expression analysis using RNA seq for bacteria ? I am looking at a genome of size 4M and genes around 3000.

Thank you.