How to count total small RNAs (known and novel) in my aligned reads?

Question

[abdul.suboor123]

I have aligned the small RNA reads with reference genome, now I want to know the method to count the total number of small RNA both (novel and know) in my reads? any method or tool please mention here, I will be thankful.

[GenoMax]

Depending on your genome you can use an applicable GFF file available at RNAcentral to count aligned reads using featureCounts.

Answer 1

[michael.ante]

Hi,

You can have a look at Genboree's exRNA Tools. They offer it as a service, but also disclose what they are doing (see below). Nevertheless, novel miRNA detection needs a bit more analysis, e.g. as in mirTools 2.0

Cheers,

Michael

Answer 2

[shawn.w.foley]

It was first developed for plant genomes, but I've had very good experience with ShortStack from the Axtell lab with both Arabidopsis and human smRNA-seq. They use weighting to assign multimappers (a vast majority of reads when performing small RNA-seq) to obtain more accurate counts for small RNA "clusters." You can then intersect these clusters with miRBase to see which correspond to annotated miRNAs and which are potentially novel.

A schematic of their mapping algorithm is below, and the publication is available here.

Answer 3

[leukosnanos]

Hi,

If you do not care about the aligner you are using, we have recently implemented an algorithm that hopefully improves the quantification of small RNA reads (and uses bowtie1 as a default aligner). The tool is called Manatee and the related paper is available here.

Cheers,

Joanna