RNa-Seq analysis

[diya]

Hi,

I am a first-time poster. I need some suggestion on the RNA-Seq analysis, but I wanted to introduce myself. I am a working professional and I am new deep-sequencing.

We are involved in the analysis of deep sequencing data, both mRNA and microRNA data. We have one experiment where we have compared mRNA deep-sequencing to microRNAs and so are interested in understanding which of the genes that change by mRNA levels are potentially regulated by the microRNAs that we also see altered. What is the best way to do this.

Your suggestions are greatly appreciated.

Thanks,

Diya

[bioinfosm]

you should be able to search around and find a lot of related information on these forums

[ulz_peter]

A good point to start is this thread:

http://seqanswers.com/forums/showthread.php?t=7068&highlight=RNA-seq

[diya]

Thank you for the reply.

Diya

[diya]

Hi,

I am trying to analyze RNA-Seq data from GAII Analyzer. When I tried to use tophat it gave an error message saying that it cannot open the .fq file. Can anyone tell me if I am doing anything wrong?

Diya