How to work with CLC Genomics Workbench software?

More Mohammad Moradzad'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

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 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

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 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

Why is the sum of the elements in a row in a Q matrix equal to zero?

When explaining substitution models, the substitutions are expressed as Q matrix. Why is the sum of the elements in a row zero?

28 February 2021 3,864 3 View

Apart from MOFA what other software is available for analysis of a multi-omic study?

Study bringing together genomics, proteomics etc together

02 February 2021 2,856 2 View

Is there any alternative to BUSCO for searching orthologues within genomes available?

I have a need to search for single-copy conservative orthologs within several plant genomes and used BUSCO tool for that. However, I found that the results produced by different versions on the...

29 January 2021 7,764 6 View

How to convert ng/ul of DNA concentration to pmol/ul ?

Dear researcher, After amplifying my target gene (1900bp) into the required cDNA by PCR,>cut specific gel bands and purify the gel and the concentration was 30ng/ul. Next, performed A-Tailing...

21 January 2021 2,671 3 View

Can use Unigenes from RNA sequences for overexpression studies (transformation) without requiring a specific plant genome?

Dear researchers: If the plant genome has not been released yet, can Unigenes from RNA sequences be used after BLAST and confirmed with known Arabidopsis genes for function/overexpression...

20 January 2021 5,557 2 View

Will these existing vaccine be effective to this new corona variant?

Suggest some good articles on Genomics of this new COVID strain.

03 January 2021 7,635 13 View

Which is the best gene editing tool among TALENs, ZFNs, CRISPR and HENs?

Since two decades we came across many tools to edit the desired gene and genome viz., clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), (2)...

27 December 2020 7,667 10 View

What is the best protocol to extract bacterial genomic DNA from cheese?

Hello everyone, Actually I am trying to extract bacterial genomic DNA from cheese. I am using isolate II genomic DNA kit. Sometimes it gives good results but sometimes I don't get anything. This...

25 December 2020 2,452 1 View

Cleaning up single cell RNA from 10x dataset?

Hello, I am new to single cell RNA data processing and am currently running my data through the initial cleanup steps via Seurat on R. I have previously done this on epithelial organoid data and...

23 December 2020 4,709 1 View

Any recommendations for a good CRISPR/Cas9 commercial system for functional genomics of fungi/yeast?

I look forward to implying a good CRISPR/Cas9 system with a selective maker for functional genomics of important genes from environmental fungi and yeast.

22 December 2020 1,432 2 View

Analysis of significance by using R programming ?

Dear All, I have the data of metabolic pathways in case and control, well there are pathways which are represented several times due to the involvement of reactions in case, well now I would...

09 December 2020 4,494 5 View

Susanta Roy

You can use CLC Genomics Workbench software to analyze RNA-seq data and single-cell sequencing data. CLC Genomics Workbench is a comprehensive bioinformatics software that offers a wide range of tools for analyzing and visualizing sequencing data. Here are some general steps to get started with RNA-seq or single-cell sequencing data analysis using CLC Genomics Workbench:

Import your sequencing data: You can import your sequencing data in various file formats, including FASTQ, BAM, or SRA. The import process varies depending on the file format and sequencing platform used. CLC Genomics Workbench provides detailed instructions on how to import different types of sequencing data.

Quality control: It is essential to assess the quality of your sequencing data to ensure that your downstream analysis is reliable. CLC Genomics Workbench provides a suite of tools to perform quality control analysis, including sequence trimming, adapter removal, and filtering of low-quality reads.

Read alignment: The next step is to align your sequencing reads to a reference genome or transcriptome. CLC Genomics Workbench provides a variety of alignment algorithms, including RNA-seq specific algorithms such as STAR and HISAT2. Additionally, CLC Genomics Workbench also provides a de novo transcriptome assembly tool to generate a reference transcriptome from your RNA-seq data.

Differential gene expression analysis: After read alignment, you can perform differential gene expression analysis to identify genes that are differentially expressed between different experimental conditions. CLC Genomics Workbench provides various statistical methods to perform differential gene expression analysis, including edgeR, DESeq2, and Limma-Voom.

Single-cell sequencing analysis: For single-cell sequencing analysis, CLC Genomics Workbench provides specialized tools such as single-cell expression analysis, cell clustering, and gene ontology enrichment analysis.

These are some general steps for analyzing RNA-seq and single-cell sequencing data using CLC Genomics Workbench. However, the exact workflow and analysis steps may vary depending on the specific research question and data type. CLC Genomics Workbench provides comprehensive documentation and tutorials to guide users through the analysis pipeline.