How to statistically test the significance of antisense-to-sense ratios using read counts from an RNA-seq experiment?

28 July 2016 1 7K Report

I have directional RNA-seq data and read count libraries derived from Bowtie2 alignments to gene-models (cDNAs) for both sense and antisense transcripts. I want to know how I can statistically test the differences in antisense-to-sense ratios between my test groups and my control groups.

Julian Spagnuolo

count data from RNA-sequencing experiments have negative binomial distributions. Also, I have replicates for each group and want to compare the ratios from one group to a control group. Not being a statistician, things get confusing quickly when trying to figure out which test to apply and how.

Badges
Science topic

More Julian Spagnuolo's questions See All

Bell's inequality from probability theory?

It is said Bell's inequality is a consequence of probability theory, which has nothing to do with quantum or not quantum. There are many papers discuss this issue, but I don't know which one is...

22 December 2020 8,254 3 View

What are the latest (theoretical) understanding of self-interference (in double-slit exp)?

In 1967 R. L. Pfleegor and L. Mandel, Phys. Lett. 24A, 766-67 proved experimentally the self-interaction of photon through double slit. Well, some said it is even later until 1986 by Grangier et...

19 November 2020 2,378 11 View

Can Copper be sputtered (via PVD) onto Platinum-Iridium to improve solderability?

Hi! First time poster on RG! I would like to solder (ball grid array reflow) onto a Platinum/Iridium alloy without the use of special Platinum soldering fluxes. Can copper be sputtered onto...

18 November 2020 2,105 3 View

Which tool for operon prediction in bacterial genomes ?

Hi, I want to predict operons on entire bacterial genomes (already annotated). I used to use operon-mapper ( https://academic.oup.com/bioinformatics/article/34/23/4118/5040321), which is great but...

07 October 2020 7,192 7 View

Can I merge z-standardized items of a 5-point and a 7-point Likert scale into one scale? (psychology)?

I am investigating a new topic with an established questionnaire. However some items are not suitable so the scales are not the best predictors in my hierarchical regression (n.s.). However, some...

04 October 2020 4,630 6 View

Optimization with Gaussian using a Cluster?

Hi all, I just try to perform a calculation for a cluster of TinOxide for determining a reaction mechanism in an organic reaction. I tried to run this calculation using a mixing basis set...

13 May 2020 8,642 4 View

Problem with Gasussian ?

Hi dear all, I just carrying out a computational run of a single point energy at MP2/6-31g++(2p,2d)//B3LYP/6-31g++(d,p), but when I tried to do the refinement at MP2/6-31g++(2p,2d) the next error...

27 March 2020 5,759 3 View

Human Cell lines with SNP genotype information?

I want to design BaseScope probes for human samples of a certain gene in his Wild-type and his mutated form (single nucleotide point mutation). To do that I need to provide stable cell lines that...

14 March 2020 3,063 2 View

Does anyone know how to do a moving heat source in cylindrical coordinates for a pipe welding simulation in ANSYS apdl?

I am doing a pipe welding simulation using the goldak model in ANSYS apdl. For doing this I would like know how can I simulate a moving heat source in cylindrical coordanates and how to implement...

05 March 2020 8,673 4 View

How can the x-ray spectrum of a spinel structure be interpreted to know Miller indices?

I have to interprete a kind of LTO samples with structure spinel in X-ray diffraction analysis but I don't know how I can get Miller indices. Thank you

11 February 2020 6,110 3 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 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

How to calculate average trend in maximum annual NDVI from MODIS?

I am wanting to calculate the average trend in maximum annual NDVI in Iceland from 2010-2020 using MODIS MYD13Q1 V6. How would I do this? I have currently inserted the NDVI bands from the MODIS...

02 March 2021 752 2 View

How can I make stacked bar graph with scatter plot?

I want to make a stacked bar graph with showing each data value as dots. I tried with graph pad prism, version 6, but could not succeed. Does anyone have tried before making such graphs?

01 March 2021 9,383 1 View

How to perform statistical analysis of coefficients extracted from transform techniques?

I am studying the potential of DCT and FFT coefficients extracted from a signal to classify the different objects that emit the signal. I applied the Shapiro-Wilk to confirm that data was not...

01 March 2021 8,079 2 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

Is anyone familiar with the cyclic compressive fatigue testing (BS EN 12697 - 25) ?

I would like to get more information on the cyclic compressive fatigue testing (BS EN 12697 - 25) which is typically done for bituminous material in pavement design. Any one can advise on the...

28 February 2021 2,004 3 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