smallRNA annotation

[NicoBxl]

Hi,

I'm lookinf for a way to annotate smallRNA from high-throughput sequencing. I've already annotate the reads with miRBase. Now I'm looking to annotate the rest of the reads ( piRNA, snoRNA,...) .

Is it a R package to do that ? or an another way ?

Thanks

N.

[NicoBxl]

nobody knows?

[steven]

nobody knows?

Have you looked in the wiki?
MirTools is listed there for instance, but i bet there are many more -hopefully the one you are looking for too.

[NicoBxl]

Thanks,

Finally here's the pipeline I used

1. annotation of the reads with miRBase 16 (blast against the reads)
2. With the rest of the reads, annotation with Rfam 10

[Palgrave]

How exactly do you go about to annotate to Rfam?

Could you please give me a detailed pipeline?

[Palgrave]

bowtie "Out of memory...."

I am trying to run bowtie on paired end reads and I am getting the following error:

Out of memory allocating the ebwt[] array for the Bowtie index. Please try
again on a computer with more memory.

Whats wrong here and what can I do without changing computer?

[NicoBxl]

how much memory do you have on your computer ? and what is the size of your genome ( is it homo sapiens ? )

[Palgrave]

I moved the thread....

[Krish_143]

How to annotate ncRNAs in bacteria (for deep sequencing data).
suggestions plz