Pratanu Kayet

23 Questions 32 Answers 0 Followers

Questions related from Pratanu Kayet

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...

05 January 2024 6,113 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...

27 September 2023 3,265 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,...

03 May 2023 9,803 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...

25 January 2023 7,474 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...

26 November 2022 3,510 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...

13 June 2022 4,171 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. :)

19 May 2022 3,116 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...

02 November 2021 7,786 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...

28 October 2021 7,965 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)...

12 May 2021 9,752 3 View

Is there any tools available to do a mutation analysis in phylogeny?

I had 1 set of 11 protein coding nucleotide sequences of 11 primates Species. and i draw a phylogenetic tree . I want to know the no of mutation has occur in each branches or want to know the...

11 March 2021 7,665 3 View

How can i calculate Date of Divergence with BEAST 1.10.4? Can anyone suggest me step by step process and parameters for making a XML file in BEAUTi?

I'm a beginner with BEAST analysis. I'm working on few Primate species and I had taken NCBI published date for tip dating. I need to calculate the date of divergence with BEAST1.10.4. also I am...

13 February 2021 1,036 7 View

To get a Branch Specific Ka/Ks value

Dose anybody Know how to get a Branch Specific Ka/Ks value? And, any good tool available for that? Thank you in advance.

01 January 1970 917 2 View

Is there any tool available which can extract a gene segment from a whole genome file?

I have 1357 whole-genome files. I wanted to extract genes from this file which 100% hit. i can use BIO-EDIT for that but this tool will take so much of time. so I want to know is there anything...

01 January 1970 6,042 2 View

Can anyone help me with RNA-Seq data analysis for DEG?

I want to perform RNA-Seq data analysis for DEG's, by taking RAW reads from the NCBI-SRA database, of DENV1, DENV2, DENV3, DENV4. I want to perform this analysis on a galaxy web server. I'm a bit...

01 January 1970 5,043 3 View

Htseq/StringTie/Featurecounts, Which is better statistically for RNA-seq data analysis?

I'm performing RNA-Seq data analysis for differentially expressed genes. as I'm new to this kind of work, so I performed these three gene count tools separately on the same bam file from RNA-Star...

01 January 1970 4,552 6 View

Getting absurd result in Datamonkey.org?

I had 11 primates gene and to know branch specific selection procedure i used aBSERLin Datamonkey.org. But data showing, w=10^9 some show two omega parameter..i align the sequences from clustal...

01 January 1970 3,116 5 View

Opposite expression pattern of same gene in different disease stages!!

I have two DEG sets for 2 disease conditions (from mild to severe condition) of the same viral infection. When I look at the common gene from these two sets of DEGs, I found that some genes show...

01 January 1970 923 13 View

Is there any in-silico methods for studying effect of up regulation and down regulation of same genes?

"Is there any in-silico methods for studying the effect of up-regulation and down-regulation of the same genes?" If yes, please suggest me the name/article.....Thank you

01 January 1970 2,083 4 View

Few quistiones related to RNA-Seq data analysis in usegalaxy/R..

I'm recently trying to perform an RNA seq data analysis and in 1st step, I faced a few questions in my mind, which I would like to understand. Please help to understand these questions. 1) In...

01 January 1970 9,082 2 View

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

I have 3 human genomes short sequencing reads of Illumina. I want to assemble these data, Can anybody suggest me a standard pipeline for this??

01 January 1970 3,376 2 View

Can i get a a human genome data that is infected with dengue1/2/3/4?

Can I get human genome data that is infected with dengue1/2/3/4? if yes, can you please suggest to me any database regarding that? can I get a m-Rana transcript there?? A big thank you in advance

01 January 1970 1,343 2 View

Downloading variants of a protein from different population...

Hi all, I want to fetch Various alleles or varients of one human protein of different populations. I want to download those alleles of one protein with their respective population information. can...

01 January 1970 8,416 2 View