what tool can i use for illumina-solexa data RNA-seq

[Xi Wang]

Hi everybody im new y this, im from mexico and i have a data from total RNAm in one condition of the bacteria R. etli the first what i see is tha some intergenic region got a read, that the orfs have diferents numbers of reads.

the cuestion is how can i normalize the data? of the RNA-seq
if i have to use RPKM?
is exist any tool to normalize the results from teh illumina?

remember that i just have the results of one condition and i think that i have to normalize this data to next compare whit other condition.



thank you everybody for your time and im sorry for the spell

I can guess what you meant to type. RPKM is recommended if you want to do the comparison between samples. A tool named "cufflink" can be used to carry out your job.

[Gamaliel]

Hi everybody im new y this, im from mexico and i have a data from total RNAm in one condition of the bacteria R. etli the first what i see is tha some intergenic region got a read, that the orfs have diferents numbers of reads.

the cuestion is how can i normalize the data? of the RNA-seq
if i have to use RPKM?
is exist any tool to normalize the results from teh illumina?

remember that i just have the results of one condition and i think that i have to normalize this data to next compare whit other condition.



thank you everybody for your time and im sorry for the spell