Please suggest me a Human Genome Assembly pipeline for Illumina short reads...

More Pratanu Kayet's questions See All

What shoud i do if multiQC stats from featurecounts show that only 3% of my aligned reads is assigned even 70% of my reads are aligned in STAR?

During my RNAseq data analysis, I encountered a problem where the statistics from MultiQC from the STAR method showed that 70% of my trimmed reads were aligned, but when I ran using the same BAM...

04 January 2024 6,157 1 View

Query regarding RNA seq data analysis?

I was performing a RNAseq data analysis. I did my alignment using RNA-STAR and then I perform featurecounts. I used latest assembly of human genome i.e. HG38.p14. But after feturecounts step i...

26 September 2023 3,278 3 View

Limit of biological replicate for RNA-seq data analysis?

I'm performing RNA-seq data analysis. I want to do healthy vs disease_stage_1, Healthy vs disease_stage_2, and Healthy vs disease_stage_3. In the case of healthy, disease_stage_1, disease_stage_2,...

02 May 2023 9,816 3 View

How to assemble human genome from illumina paired end sequencing?

I have 3 Illumina paired-end sequencing data of humans. I want to assemble these 3 genomes. My final goal is to retrieve some gene sequences from these 3 genomes. So, 1) Please suggest to me any...

24 January 2023 7,493 4 View

Can someone please explain the interpretation of Nucleotide Diversity (Pi) value for a viral Alignment file?

I used DnaSP software to perform a nucleotide diversity analysis on a viral alignment file. After observing the data I saw that some positions have high values (0.79) and some positions have lower...

25 November 2022 3,522 1 View

Can anybody suggest me a pipeline to assemble chromosome specific human genome?

I have human WGS raw reads and paired-end data. Illumina Hi-Seq 2000 was used for sequencing. I want to assemble this genome either de-novo or reference-based. I want to assemble it...

12 June 2022 4,218 3 View

Is there any tool or web server available for prediction of mutational hotspot in a RNA?

Can anybody suggest to me any tool or web server, that can predict a probable mutational hot spot?? A big Thank you in advance. :)

18 May 2022 3,132 2 View

How can I run a sequence identity analysis or clustering of 2 million sequence?

Hi, I have over 2 million nucleotide sequence and each sequence is average 30kb in size. I want to run A sequence identity and clustering analysis on that..I tried CD-HIT suite but it falling...

01 November 2021 7,799 4 View

Is there any way to download all whole genome at once from GISAID database instade of 10k per time???

I'm trying to download whole genome of alpha strain COVID-19 from GISAID database.in alpha strain 2 million sequence are there.and in that database, it is showing that I can download max 10k per...

27 October 2021 7,976 1 View

Tools to perform whole genome clustering by 100% sequence identity?

I have whole genome data sets of SARS-Cov2 of different countries. Now I want to exclude genome sequences which represents 100% sequence similarity. I want to do it by clustering analysis.. 1)...

11 May 2021 9,763 3 View

Who of all the Global Scientific community will help me Prof. Dr. Yoshida make way for TPEOM, MEC ~EMC to return the atmospheric gases to the norma ?

TEP presentation caption (The Environmental Project) Re: Why should Washington’s DC, or any country government point of location think of as nowadays of as to being 'tomorrow as to come! if it...

03 August 2024 2,484 1 View

Which is more important: The human factor or the technological factor in combating climate change?

On a personal note, even though technology has attracted a lot of interest and funding to combat climate change, it is becoming more and more clear that taking care of the "Human Dimension" is...

02 August 2024 6,773 12 View

How is the bacterial genome's high protein count verified as genuine despite 800+ contigs and good metrics (98.55%completeness, 0.68% contamination)?

Given that the bacterial genome has over 800 contigs, but its quality metrics are good, with a completeness of 98.55% and a contamination of 0.68% as assessed by CheckM, what specific validation...

01 August 2024 1,514 1 View

How to retain the a GFP tagged gene expression in stable cell line?

Hello , I established a stable cell line expressing GFP tagged to a centrosomal gene having G418 drug selection marker. I validated the stable line by IFA and Western blotting, results are fine....

29 July 2024 5,007 0 View

Recovery Viurses from bacteria genome?

Hello everyone, I am currently looking for tools to recovery viral genomes from bacterial genomes, not metagenomes. However, I have only found tools that are designed for retrieving and studying...

28 July 2024 8,953 1 View

In terms of chaos, what is the necessary and sufficient condition for authoritarianism, permanent or temporary, to come to exist and persist?

Since 2016 Brexit, the world needed to change the thinking behind traditional democracy as the democratic landscape changed, yet traditional democratic thinkers and actors have been acting as if...

28 July 2024 6,515 1 View

What is effective targeted chaos?

Perfect democracy thinking assumes no chaos so no need for independent rule of law system and liberal democracies assume the possibility of normal democratic chaos that can be sorted out by an...

28 July 2024 473 1 View

I want to get updates regarding international law, international trade law, international institutions and human rights etc?

Please send me updates regarding the above-mentioned areas in the question mark?

28 July 2024 5,197 3 View

Why my negative control siRNA is decreasing the target gene's expression?

Hi Everyone, I'm using an siRNA kit to knock down a target gene. The kit guarantees that the negative control doesn't target any sequence in mouse genome, and when I use BLAST I don't find any...

23 July 2024 2,673 6 View

How does the human microbiome influence health and disease, including implications for personalized medicine and microbiome-targeted therapies?

Probiotics related.

22 July 2024 1,707 2 View