Can you help with the separation of HCV genome from Illumina FASTQ dataset?

06 June 2014 1 5K Report

I have FASTQ files as whole genome dataset from illumina I need to extract Viral whole genome for HCV type 4 from my dataset.

What can I do?

Srinivas M Srikanth

Hi,

I am not sure the whole genome data you have corresponds to what?, if it is for the HCV genome then its simple, you can align the fastq against the genome and find the reads. On the contrary, if the reads are for human genome , you need to align the reads to human genome first and then get the unmapped reads. You these reads to align against the HCV genome (you may get some answers). Hope this helps..

Srikanth

Badges
Science method

More Elsayed Hegazy's questions See All

Any recommendation regarding individual genome sequencing publications or tools ?

I have 9 VCF files for individuals i need some publications or tools to know more about:- - Disease risk calculations. - Disease identification. - Drug response. - Antibiotic resistance. - Dealing...

03 April 2018 482 2 View

Can someone advise on Galaxy installation on Ubuntu or alternative tool for NGS?

I follow all steps and Ubuntu terminal commands to install Galaxy but it hang on step (serving on 8080 localhost) without any response and when I access the localhost : 8080 I found galaxy with...

06 July 2013 9,775 4 View

I need to know step by step instructions about using MATLAB for Mass Spec data analysis...

- Something like how to import RAW files to MATLAB - How to align peaks - How to visualize peaks - How to identify proteins - How to quantify proteins - How to filter peaks best regards,

05 June 2012 1,552 8 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

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 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

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature)?

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature-based reflection)? Thank you for your time and for...

03 March 2021 2,870 3 View

What degree of missing data in a particular case/participant results in Expectation-Maximisation no longer working?

I'm dealing with a mediation model and am using the PROCESS module in SPSS. Due to SPSS and PROCESS being limited in the imputation methods - being unable to handle multiple imputation - the other...

02 March 2021 4,362 1 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Sample dilution for quantitative analysis using ELISA?

If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis

02 March 2021 7,670 3 View