RNA-Seq, software stats

[dukevn]

Hi folks,

Forgive me if somebody already did this before. I am newbie to RNA-Seq, and I am really curious what softwares people are using together with what options they use. This resources will be very helpful for everyone, especially people working with RNA-Seq. So, there are mainly two points in here:

* What software(s) you use, and
* What option(s) you find the best with that software(s)

Please, do not tell me going to some posts listing softwares, because I already know that. So, if you are interested in contribution, please shout out here!!!

Thanks,

D.

[kjod71]

commercial software I've been trying

Hi,

I'm a newbie to RNA-seq too and I have been using Galaxy as well as trial versions of CLC Bio, GenomeQuest, NextGENe (Soft Genetics) and Partek with varying degrees of success. For my purposes now, all I want are gene lists of what is up/down in my different conditions and CLC and Genome Quest gave me answers pretty quickly. NextGENe and Partek have so far required more tweaking. And Galaxy has been very useful in so far as I can now Map my reads to the UCSC browser. However, these mapped reads are raw reads and not normalized values (RPKM). I am trying to figure out how to map normalized values on the UCSC browser.

KevNYC

[dukevn]

Hi,

I'm a newbie to RNA-seq too and I have been using Galaxy as well as trial versions of CLC Bio, GenomeQuest, NextGENe (Soft Genetics) and Partek with varying degrees of success. For my purposes now, all I want are gene lists of what is up/down in my different conditions and CLC and Genome Quest gave me answers pretty quickly. NextGENe and Partek have so far required more tweaking. And Galaxy has been very useful in so far as I can now Map my reads to the UCSC browser. However, these mapped reads are raw reads and not normalized values (RPKM). I am trying to figure out how to map normalized values on the UCSC browser.

KevNYC

Great! Thanks KevNYC for your experience. I tend to use open source/free softwares, so I have never tried (even trial) any of those that you tried, but I might give it a second thought.

Anyway, I have been playing with TopHat, CuffLinks, DEGseq. In terms of finding enrich/interested regions (peaks), I have been also trying CisGenome, MACS. Maybe I am still new to the field, and I am not very good at programming... but my feeling is that none of them gives me a satisfied result.

I am going to try ERANGE, but it looks quite challenging to me .

D.

[kjod71]

Hi D,

Glad to hear it. I haven't done any programming myself and am hoping to collaborate with someone for that.

Best,

KevNYC