How to count total small RNAs (known and novel) in my aligned reads?
3
0
Entering edit mode
2.1 years ago

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.

sRNA small RNA counts • 1.1k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
2.1 years ago
michael.ante ★ 3.7k

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

Workflow

ADD COMMENT
0
Entering edit mode
2.1 years ago
shawn.w.foley ★ 1.3k

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.

enter image description here

ADD COMMENT
0
Entering edit mode
20 months ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 2599 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6