New to RNAseq

[waseem]

Hello
I am new to RNAseq analysis.
Jut got my sequences and I want to start.
I want to allign the reads to reference transcriptome.
Any guidelines or help for a beginner.

[nirvana]

Maybe you could begin with trying some align softwares, such as BWA

[pbluescript]

Watch some tutorial videos at Galaxy:

http://main.g2.bx.psu.edu/

Or, if you're comfortable with the command line, jump right in with something like Tophat.

[ttnguyen]

There is a tutorial for the analysis of RNA-seq data:

http://seqanswers.com/forums/showthread.php?t=7068

[waseem]

Thank you very much.
It helped a lot.
Next I wanted to do is "to identify polymorphisms in arabidopsis genome" and I have paired end DNA sequences. any hint about where to start?

[pbluescript]

The two main programs people use for SNP detection are samtools and GATK. I'd start with reading the manuals for those.