2 replies to this topic

[eurowall]

Hi everyone,

I have been working on the microRNA deep sequencing with Solexa/Illumina platform. This is supposed to be the most advanced technology for microRNA sequencing.

I have got a problem: What program I should use to analyse the raw data?? miRDeep?? How to define the known miRNA? From miRbase??

Thank you so much for your advice

Max

[ishmael]

eurowall, on Jul 1 2009, 05:49 PM, said:

Hi everyone,

I have been working on the microRNA deep sequencing with Solexa/Illumina platform. This is supposed to be the most advanced technology for microRNA sequencing.

I have got a problem: What program I should use to analyse the raw data?? miRDeep?? How to define the known miRNA? From miRbase??

Thank you so much for your advice

Max

For the first step, you may use bowtie or soap2 to map the small RNAs to the genome.
miRDeep is a method to find known and novel miRs.
For known miRs, you may use miRBase as refrence.

[Katerina]

Hi all!))

I also work with the microRNA deep sequencing (SOLiD platform), and I have some questions:
which level of noise is observed for mapping reads to the DB? How you normalized you data?

and maybe someone of you knows how much classes of miRNA can arabidopsis contain at the same time(approximate)?

thanks for the reply))