Question: Estimating the distribution of small non-coding RNAs among the reads: Which annotation database / r-Package?
0
gravatar for f.fassihian
3.5 years ago by
f.fassihian20
Germany
f.fassihian20 wrote:

Hi everybody,

I am working on miRNAs derived from plasma exosomes. I have already mapped my small RNA sequences against human genome and mature miRNAs from mirBase to get the known miRNAs. Now, I would like to annotate the reads that could not be identified as miRNAs to find the distribution of other RNA species in the exosomes. Could somebody suggest me an R package for annotation or an annotation database for other RNA species? (I have already used blastn to detect other small non-coding RNAs. But this does not help me to get what I mentioned above.)

Many thanks in advance

ADD COMMENTlink modified 3.4 years ago • written 3.5 years ago by f.fassihian20
1
gravatar for Damian Kao
3.5 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

RFAM (http://rfam.xfam.org/) has a collection of various RNA classifications. You'll probably have to navigate their ftp data files to find specifically what you are looking for though.

ADD COMMENTlink written 3.5 years ago by Damian Kao15k
0
gravatar for f.fassihian
3.4 years ago by
f.fassihian20
Germany
f.fassihian20 wrote:

Thanks a lot for your tips! I'm going to use RFAM.

ADD COMMENTlink written 3.4 years ago by f.fassihian20
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