Question: MDS plot for miRNA data
gravatar for Adrian Pelin
4.2 years ago by
Adrian Pelin2.3k
Adrian Pelin2.3k wrote:


I have sequenced human miRNA (total RNA enriched for 15-25nt) in different conditions. I mapped my reads with a minimum overlap of 15 + perfect match to the human genome, and extracted read counts using bedtools of miRBase miRNA annotations.

I now want to generally compare my different conditions and see which ones are more similar to each other at the small RNA level. I remember it is possible to do that with cummeRBound package in R, but it require cufflinks output, and it is my understanding that cufflinks is not necessarly a good option for miRNA.

Anyone have any idea how to do this?

Also, I read in some papers that people add a pseudocount of 1 to all read counts so as not to encounter division by 0 errors.



rna-seq mds smallrna • 1.2k views
ADD COMMENTlink written 4.2 years ago by Adrian Pelin2.3k

Bioconductor's RNAseq workflow may be of help. There are sections on PCA and MDS, and the data expected are just read counts, so your bedtools counts should suffice.

ADD REPLYlink written 4.2 years ago by h.mon28k

Nice, I see it. Thanks, this is the answer.

ADD REPLYlink written 4.2 years ago by Adrian Pelin2.3k
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