Is there any software that will help to present the read coverage in the form of graphs?Could anybody kindly help me to resolve the issue?

I am mapping the raw reads to the contigs generated by de novo assembly of the same reads and want to represent the read coverage in the form of graph..

08 September 2016 9,893 6 View

Can anybody help me to run AfterQC for NGS sequence data quality check?

08 September 2016 1,083 1 View

Could anybody help me to overcome the DNA isolation problem from fish gut content?

04 May 2016 8,466 6 View

How to validate the putative SNPs? Which method is suitable for this purpose?

SNPs are abundant in the genome of any organism. We are in the process of SNP development through RNA-seq. We want to validate them by taking a panel of 48 unrelated individuals. The polymorphic...

07 August 2013 4,732 7 View

I am working in window based systems and want to load ubunto onto my PC. Can anyone kindly help me?

Since almost all the programs used for NGS data analysis are runing in linux environment, Linux (like Ubunto) is to be loaded in the PC.

04 May 2013 4,720 7 View

How to calculate sex specific recombination frequency?

I am using Joinmap version 4.1 for linkage analysis in F1 mapping population using microsatellite markers. While analysing I was not able to calculate sex specific recombination frequency...

03 April 2013 8,523 0 View

I am using an F1 mapping panel for linkage analysis

Microsatellites are the choice of markers in many non model organisms for linkage map construction. I am working on a non model fish species and developed around 140 informative markers in order...

01 February 2013 4,146 6 View

Construction of genetic map is based on recombination frequencies.

I am working on construction of genetic map of a fish species using LINKMFEX software. Could any body guide explain why recombination frequency differes in Male amd Female parents and how to...

08 September 2012 6,023 0 View

I wish to clone and characterize a gene in a species in which its sequence is not available. Can anyone suggest how I can proceed?

Since its sequence information is not available which method should I follow?

03 April 2012 2,107 4 View

Can any one please explain in detais about QTL mapping in F2 design?

Linkage based QTL mapping is one of the hot topic now adays.

10 November 2011 8,325 1 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

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

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

RNA degraded after good nanodrop readings?

23 February 2021 8,850 2 View

Is there a way to extract total RNA and protein from cell culture at the same time, without denaturing protein?

Hi all, Is there a way to extract RNA and protein from the same cell culture sample? Because we need to use the protein for gelatin zymography at later time, we are looking for a method that can...

22 February 2021 5,341 5 View