To get a Branch Specific Ka/Ks value

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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

Weak DAPI staining after immunohistochemistry - how to improve?

After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...

05 August 2024 9,637 2 View

The Curse of Evolution and Complexity?

Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...

05 August 2024 6,247 3 View

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 View

Could you try using PeptiCloud and see if it's a useful tool for biology research?

PeptiCloud (www.pepticloud.com) is a bioinformatic platform that allows researchers to organize and share their data for their projects as well as collaborate with others in one place. Through...

28 July 2024 4,762 2 View

Do you know of any online international conferences that offer free discussions?

Do you know of any online international conferences that offer free discussions? I am looking for examples in the field of molecular ecology and DIY biology.

28 July 2024 6,501 0 View

Illustra™ MicroSpin™ G-25 columns what it is used for?

Hello, We found three packages of Illustra™ MicroSpin™ G-25 columns in the cabinet of an unused lab. They are very old but have never been opened. I have never used this kit before, and I couldn't...

25 July 2024 4,927 3 View

Pink bacterial colonies?

I am cloning an overexpression plasmid with my protein of interest tagged with mScarlet. After transforming my ligated product into DH5α bacteria and plating on LB agar, I noticed colonies with a...

22 July 2024 5,953 6 View

How are clinical and environmental yeast/fungal strains stored usually in mycology laboratories?

I understand a glycerol stock for long-term preservation would be ideal, but how are working cultures generally stored? Mainly concerning Candida spp. isolates. A few references mention that they...

22 July 2024 6,592 3 View

How to use evolutionary algorithms with real parameters in ryu sdn controller with large scale?

Hi, I wanna to implement evolutionary algorithms in ryu sdn controller in mininet, i have some challenges, how i can run the big scale topo with one sdn contoller??? and another question is to...

21 July 2024 246 2 View

Please, from the computational calculations of an organic compounds using Gaussian program?

Using DFT/B3LYP/6-311++G

17 July 2024 7,720 1 View