Why very low percentage of reads are assigned to miRNA category by sRNAbench?

12 March 2020 1 446 Report

Hi,

I have miRNA Seq data. I am trying to predict miRNA from this data. However, I have seen almost half of the reads belong to 19-22bp (sequence length distribution) and another peak is detected at 32bp (I am assuming the possibility of piRNA). I am using sRNAbench for my analysis and I can find that more than 90% of reads are aligning into the reference genome. However, a very low percentage of reads are assigned for miRNA, details are the following:

Detected mature miR:2 (0.08%) Detected hairpin miR:2 (0.1%)Reads mapped to miRNAs:4 (0.0%)Reads mapped to miRBase hairpins:2 (0.0%).

Is it normal ? or I am missing something somewhere?

Sura Aldewachi

interesting question

Badges
Science topic

More Amarinder Singh Thind's questions See All

mRNA transcripts measured by RNAseq represent cell transcriptome of pre or post-interaction with miRNA?

I have a very basic question as mentioned in the question when RNAseq technology measures the mRNA abundance if it is acquired after degradation of dsRNA by miRNA or before? I would like to...

25 August 2020 5,050 4 View

What are the resources of the RNAseq data to retrieve the data of different stages of one particular cancer?

25 April 2016 2,172 2 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

MiRNA qpcr problem?

Dear All, mirna primer showing some problem in the melting curve? any idea why? As attached is the melting curve. The forward sequence is obtained from miRBase and reverse primer is universal.

28 February 2021 5,008 4 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

Can MicroRNA cross the blood brain barrier?

In diseased conditions, many genes and gene products are visible in the bloodstream. So my question is whether we can find traces of microRNA which is involved in disease and disorder in blood serum?

24 February 2021 7,064 3 View

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View