Tetraploids, diploids and SNPs calling from PE-RAD sequencing approach

19 July 2017 0 8K Report

Hi Folks!

We have generated reads from different individuals (including diploids+polypolids+ all are non-model) through ddRAD library by using MiSeq plateform through PE sequencing approach. Can anyone suggests that which pipeline we can use to call the SNPs (inter-homoeologue

polymorphisms (IHP) for polyploid) and loci confidently and correctly.

Thanks in Advance

Badges
Science topic

Similar topics
Mathematical Sciences
Graphs

More Gulzar Khan's questions See All

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

Hello fellow researcher .. What is the meaning of your name?

I would like to create a small guide containing the meanings of the names .. Thanks to everyone who cooperates with me in achieving it.

03 March 2021 5,266 4 View

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

Is There Any Feasible Method To Test The Efficiency Of Fluorescent Compounds Other Than UV Spectrometers ? Suggestions Would Be Appreciated !

02 March 2021 5,785 3 View

Is it possible to do piezoelectric coupling in ANSYS-APDL or COMSOL between tapered substrate and rectangular piezoelectric patch?

How to do Piezoelectric coupling in ANSYS-APDL or COMSOL between tapered substrate and rectangular piezoelectric patch? Piezoelectric coupling between the rectangular substrate and rectangular...

02 March 2021 9,833 3 View

Why the results when using wall thickness and when using shell conduction are different in ansys fluent?

Actually, I am running cfd simulation for a heat exchanger which has two fluids one hot and other one is cold fluid. there is a solid domain between them, which I removed and instead I have used...

01 March 2021 9,537 2 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Adherance of Polyaniline coating over stainless steel?

Is the electropolymerisation of polyaniline coating over stainless steel (SS) via Cyclic voltammetry technique is really adherant? Else how to improve the adhesion of the coating, whether any...

01 March 2021 8,220 2 View

How much pressure we can reduce at the outlet to avoid Reverse Flow?

I am simulating Heat Exchanger. I have tried and tested all the methods to resolve this issue from the internet like refining mesh, improving skewness and orthogonal quality ,extending outlet to...

01 March 2021 6,985 3 View

How can you bring two structures together to create an adhesive bond in LAMMPS?

I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created....

01 March 2021 3,325 2 View

No title

Does anyone have the experience of using Taq Man probes in the QIAGEN Rotar- Gene qPCR machine?

01 March 2021 5,311 1 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

How do I check the quality of my viral RNA prior to metagenomic sequencing?

I am doing metagenomic sequencing without enrichment for an RNA virus. After my RNA is extracted from the blood I am doing library prep with the NEBNext Ultra directional RNA library prep kit for...

16 February 2021 5,101 2 View

How to remove the species data from rda data frame in R (only remain the sites/samples point)?

Dear everyone, When I using the rda function in r, I met this question. As you can see in the figure, there are a lot of deep blue points which refers to the species. But I would like remain...

15 February 2021 8,982 2 View

Which and How to use teaching strategies and procedures to effectively integrate the four skills while teaching English Language Online?

As an inexperienced teacher in the field of online teaching, I have the fear of unconsciously ignoring one of the skills while focusing on not ignoring the other! Therefore, I wish to make use of...

09 February 2021 5,101 4 View

How to obtain confidence intervals in Amos?

Dear all, I would like to know your opinion on the following issue I am struggling with. I am estimating a multigroup model with several factors all correlated among them (they represent...

04 February 2021 1,381 4 View

How do we calculate 95% confidence intervals for RMSE?

I have two datasets (measured and modelled). I want to calculate 95% confidence intervals for RMSE. Cany anyone please help me with this? Thank you in advance

04 February 2021 5,439 6 View

How to find statistical data of EEG signals?

Hi all, I hope everyone is doing good. I am working on Machine Learning, I am working on EEG data for which I have to extract statistical features of the data. Using mne library I have extracted...

29 January 2021 6,686 1 View

Cutoff for asv reads?

I got my fungi sequences back from Illumina Miseq sequencing and I'm wondering how many reads do you use as a cutoff? ie. do you delete anything with less than 100 reads? I can't seem to find any...

28 January 2021 5,646 4 View

My question is that how can we select the unique peptides ?

Hi all Scientists; I have similar question. Can you please help me in selecting unique/distinct peptides in case of LC-MS/MS analysis? I have done salivary gland proteomes for...

26 January 2021 7,488 3 View