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How to merge STAR output reads Counts

Merging STAR output reads Counts “”

How to merge STAR output reads Counts “”?

The output files of STAR (from option –quantMode GeneCounts) contain 4 columns that correspond to different counts per gene calculated according to the protocol’s strandedness

column 1: gene ID

column 2: counts for unstranded RNA-seq.

column 3: counts for the 1st read strand aligned with RNA

column 4: counts for the 2nd read strand aligned with RNA

Run following script to merge all files:

files = list.files(paste0(‘/AllRNAseqdata/test/’), “*$”, full.names = T)

countData = data.frame(fread(files[1]))[c(1,4)]

for(i in 2:length(files)) {
countData = cbind(countData, data.frame(fread(files[i]))[4])
###Skip first 4 lines, count data starts on the 5th line

countData = countData[c(5:nrow(countData)),]

colnames(countData) = c(“GeneID”, gsub(paste0(‘/AllRNAseqdata/test//’), “”, files))

colnames(countData) = gsub(“”, “”, colnames(countData))
rownames(countData) = countData$GeneID
countData = countData[,c(2:ncol(countData))]
write.table(countData, file=”counts.txt”, quote=F,sep=’\t’,row.names=T, col.names=T)

Polio is re-emerging worldwide

Polio is re-emerging worldwide

Recently, researchers have detected the poliovirus in the sewage system in east London on a number of occasions this year. Its original source is likely to be someone recently inoculated with an oral version of the polio vaccine. But according to WHO report cases due to wild poliovirus have decreased by over 99% since 1988, from an estimated 350 000 cases then, to 6 reported cases in 2021.

The discovery of poliovirus in New York state, London and Jerusalem this year has taken many by surprise but public-health researchers fighting to eradicate the disease say it was only a matter of time.

The virus found in these regions is derived from an oral polio vaccine used in some countries. So far, only two cases of polio-related paralysis have been reported, in Jerusalem in February and New York in June1; the New York infection was the first such US case in nearly a decade. But wastewater samples in all three areas suggest that the virus is circulating more widely.

What are Polio symptoms ?

The majority of people with the infection have no symptoms but some feel as if they have the flu, with:

> a high temperature
> sore throat
> headache
> stomach pain
> aching muscles
> feeling sick

Why are these outbreaks happening?

The most obvious explanation for the reemergence of polio in some countries are that only about 50 percent of residents are vaccinated against polio. Most unvaccinated people who contract the virus don’t get sick at all or have mild illness, and about 25 percent will get mild flu-like symptoms. There’s two main forms of polio virus: There’s the wild-type virus, which is seen in endemic countries, then there’s what’s known as vaccine-derived polio — the type detected in New York and London’s wastewater.

Further readings:

What polio’s UK presence means for global health

Spate of polio outbreaks worldwide puts scientists on alert

Poliovirus in London sewage sparks alarm

Human Microbiome in Health and Disease

Human Microbiome in Health and Disease

Human biology can no longer concern itself only with human cells: Microbiomes at different body sites and functional metagenomics must be considered part of systems biology. The emergence of metagenomics has resulted in the generation of vast data sets of microbial genes and pathways present in different body habitats.

The microbiome is the collection of all microbes, such as bacteria, fungi, viruses, and their genes, that naturally live on our bodies and inside us. Interest in the role of the microbiome in human health has burgeoned over the past decade with the advent of new technologies for interrogating complex microbial communities. The large-scale dynamics of the microbiome can be described by many of the tools and observations used in the study of population ecology.

Metagenomics examines the structure and functional potential of microbial communities in their native habitats through the direct isolation and analysis of community DNA. In inflammatory bowel disease, gut microbiome studies have shown an association with perturbations in community composition and, especially, function.

How can the microbiome affect health?

Microbiota stimulate the immune system, break down potentially toxic food compounds, and synthesize certain vitamins and amino acids, including the B vitamins and vitamin K. For example, the key enzymes needed to form vitamin B12 are only found in bacteria, not in plants and animals.

A person’s core microbiome is formed in the first years of life but can change over time in response to different factors including diet, medications, and environmental exposures. Differences in the microbiome may lead to different health effects from environmental exposures and may also help determine individual susceptibility to certain illnesses.

Dietary prebiotics have been defined as “a selectively fermented ingredient that results in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health”

The microbiota of a healthy person will also provide protection from pathogenic organisms that enter the body such as through drinking or eating contaminated water or food.

Human Microbiome data:

The tremendous expansion of information collected on the human microbiome in recent years is highlighted by data generated through several large-scale endeavors to characterize the human microbiome, namely the European Metagenomics of the Human Intestinal Tract (MetaHIT) and the NIH-funded Human Microbiome Project (HMP).

The Common Fund’s Human Microbiome Project (HMP) developed research resources to enable the study of the microbial communities that live in and on our bodies and the roles they play in human health and disease.


Pflughoeft KJ, Versalovic J. Human microbiome in health and disease. Annu Rev Pathol. 2012;7:99-122. doi: 10.1146/annurev-pathol-011811-132421. Epub 2011 Sep 9. PMID: 21910623.

Shreiner AB, Kao JY, Young VB. The gut microbiome in health and in disease. Curr Opin Gastroenterol. 2015 Jan;31(1):69-75. doi: 10.1097/MOG.0000000000000139. PMID: 25394236; PMCID: PMC4290017.



What are PFASs ?
Per- and polyfluoroalkyl substances (PFAS) are a diverse group of human-made chemicals used in a wide range of consumer and industrial products. PFASs have multiple fluorine atoms attached to an alkyl chain. There are total 4,730 distinct PFASs are known with at least three perfluorinated carbon atoms.

Research involving humans suggests that high levels of certain PFAS may lead to the following:
Increased cholesterol levels
Changes in liver enzymes
Small decreases in infant birth weights
Decreased vaccine response in children
Increased risk of high blood pressure or pre-eclampsia in pregnant women
Increased risk of kidney or testicular cancer

Sudden increase in Global mysterious Hepatitis Cases in Children

Sudden increase in Global mysterious Hepatitis Cases in Children

The number of mysterious cases of acute hepatitis in children continues to grow, with hundreds of incidences now being reported worldwide. Although cases have been reported across multiple continents, most have been reported in the United Kingdom. Scientists and healthcare professionals around the world are continuing to investigate a sudden increase in hepatitis cases in children. Acute hepatitis in children is certainly not new, and it can be worrisome. Successful worldwide vaccination campaigns over the past few decades have led to demonstrable improvements in public health and well-being by reducing the incidence and consequences of two viral causes -hepatitis A and B viruses. Hepatitis is a condition that affects the liver and can be caused by infection with a virus.

Six hundred and fifty probable cases of acute hepatitis of unknown aetiology in children have been reported to WHO from 33 countries in five WHO Regions between 5 April and 26 May 2022. (According to WHO report)

There are several viruses that can infect the liver, the best-known being hepatitis A, B, C, D and E. These viruses are all quite different – some of them can be prevented by vaccination and some can be treated with antiviral therapies.

What are common symptoms of Hepatitis?

Yellowing of the white parts of the eyes or skin (jaundice), Dark urine, pale grey colored faces, itchy skin, muscle and joint pain, a high tempreture etc

What could be causing the outbreak?

Initial findings suggest that an adenovirus – a common type of virus that causes a range of symptoms and illnesses

Could the cases be linked to COVID-19 infection or vaccine?

There is no link between these hepatitis cases and the COVID-19 vaccine. The COVID-19 vaccines do not contain viruses that can grow in the human body. There were no COVID-19 vaccinations recorded in cases under 5, the age group which makes up over 75% of hepatitis cases.


  1. Clinical Spectrum of Children with Acute Hepatitis of Unknown Cause
    N Engl J Med 2022; 387:611-619 DOI: 10.1056/NEJMoa2206704
  2. Kelly, D.A., Stamataki, Z. Sudden onset hepatitis in children. Nat Rev Gastroenterol Hepatol (2022).

Useful information:

  1. Hepatitis outbreak in children: What do we know so far?
  2. Mysterious hepatitis outbreak sickens young children in Europe as CDC probes cases in Alabama
  3. Acute hepatitis of unknown aetiology in children – Multi-country

UK Biobank 2022

What is UK Biobank?

UK Biobank is a large-scale biomedical database and research resource that is enabling new scientific discoveries to be made that improve public health. The database is regularly augmented with additional data and is globally accessible to approved researchers undertaking vital research into the most common and life-threatening diseases. It is a major contributor to the advancement of modern medicine and treatment and has enabled several scientific discoveries that improve human health.

UK Biobank is a world-leading biomedical database to enable scientific discoveries that improve human health. Our goal is to inspire the imaginations of health researchers around the world to meet the challenge of greater understanding, prevention, and treatment of a range of serious illnesses. UK Biobank has Research Tissue Bank Approval till 2026 and through access to an unmatched amount of biological and medical data on half a million people living in the UK, we can enable your vision of improving human health.

1. UK Biobank is a longitudinal study; it follows the health of 500,000 volunteer participants.

2. Participants were aged between 40-69 years when they joined UK Biobank between 2006-2010.

3. Each participant attended a baseline assessment at a centre in England (89%), Scotland (7%) and Wales (4%).

4. Participants provided their consent for long-term follow-up.

5. Participants answered lots of questions about their health & lifestyle.

6. Participants donated samples of blood, urine and saliva for long-term storage and analysis.

Health records

On joining UK Biobank, participants consented to have their health followed over many years through linkage to their health-related records. UK Biobank has linked to cancer and death registry data, hospital inpatient admissions and primary care records. These data are generally updated annually.  Researchers are helping UK Biobank to develop algorithms to identify common disorders such as stroke, heart disease and dementia.


UK Biobank has received funding from government, charity and industry to extract a range of genetic data from participant samples.

  • Genotyping using Affymetrix microarray
  • Whole Exome Sequencing
  • Whole Genome Sequencing

Accessing the UK Biobank resource

Since 2012, bona fide researchers can apply to access the UK Biobank research resource to conduct health-related research that is in the public interest.  As UK Biobank continues to release additional data relating to our participants (such as data on genetics, imaging and health records) interest in the resource has grown.  UK Biobank welcomes applications from the UK and overseas and from academia and industry.

Final data release from the world’s largest whole exome sequencing project:

UK Biobank has today added the final tranche of exome sequencing data to its research database. This represents completion of cohort-wide exome sequencing for over 470,000 participants within the UK Biobank resource. These de-identified data can now be accessed by approved researchers through the cloud-based UK Biobank Research Analysis Platform. The generation of whole exome sequencing data was made possible through collaboration and funding support from the UK Biobank Exome Sequencing Consortium (UKB-ESC).

The consortium comprises of Regeneron Pharmaceuticals, AbbVie, Alnylam Pharmaceuticals, AstraZeneca, Biogen, Bristol Myers Squibb, Pfizer and Takeda. This unique collaboration has resulted in the largest exome dataset in the world and will be transformative for studying the genetic determinants of disease. Reference: UK Biobank

More information



Study suggesting that cellular and tissue function can be reactivates in pigs after death

10 ways to sleep better in unbearable heat

The new English Premier League season 2022

Study suggesting that cellular and tissue function can be reactivates in pigs after death

Without oxygen, mammalian cells die. Paradoxically, restoring oxygen to cells that have been deprived of it also causes stress and damage — a phenomenon called reperfusion or reoxygenation injury. For decades, scientists have been searching for strategies to protect cells and organs against the detrimental effects of oxygen deprivation and reintroduction that can occur following stroke, heart attack or the cessation of breathing. Writing in Nature, Andrijevic et al. describe a system called OrganEx that enables oxygen to be recirculated throughout a pig’s body, preserving cells and organs an hour after a cardiac arrest.

Prof Martin Monti, Professor of Cognitive Psychology, University of California Los Angeles (UCLA), said:
“Biological death is more like a cascade of dominoes, with one event triggering the next, than an instantaneous transition. What is ground-breaking about this technology is that this cascade can be halted in some organs if only the right cellular environment and metabolic parameters can be restored. The potential implications, if this will ever be successfully translated to humans, are huge: how many more lives could be saved through transplantation each year thanks to greater organ viability?

Dr Anders Sandberg, Senior Research Fellow at the Future of Humanity Institute, University of Oxford, said:

“When blood circulation stops, cells begin to die due to lack of oxygen, and chemical changes begin that harm tissues and organ function. At normal temperature, irreversible changes set in after a few minutes. What this paper shows is that significant improvements are possible in how long after death preservation methods to keep organs alive can be started (up to an hour), and that some of the cellular damage can be partially reversed.

In the current study, Andrijevic et al. optimized this perfusate for whole-body reperfusion, altering the cryoprotective agents and antibiotics it contained, among other changes. They pumped their perfusate through the body using a computer-controlled system that involved a perfusion pump, an oxygenator and a haemodialysis unit, which maintains stable levels of electrolytes and other essential molecules in the perfusate.

10 ways to sleep better in unbearable heat

Is the mid year heat making it hard to get some rest? Awaken feeling revived and invigorated with these tips and deceives on the most proficient method to keep it cool when the evenings are sweltering and tacky. While summer's perfect for open air tomfoolery or finding companions, around evening time while you're attempting to hit the hay you might find it harder to settle in and nod off.

Getting a familiar night's rest in an intensity wave can be precarious - however did you had at least some idea that the temperature of both your body and your environmental elements can influence the nature of your rest? Heat doesn't simply make it hard to nod off - it additionally influences how well you rest.

Here are a few helpful hints to keep you cool and rest more straightforward this mid year.

1. Keep the sunlight and heat out 

Close drapes and windows (especially those not facing north) during the hottest and brightest hours of the day. In the summer, this generally means the hours between 12 and 4:30 p.m., depending on your location and other weather conditions like wind and cloud cover. This will prevent heat from entering and getting trapped in your home.

2. Open the windows

On the off chance that your room is hotter than outside, leave the windows open around evening time to allow in a new breeze. Night air will in general get cooler in the early hours. The outside air can assist with holding the temperature down and prevent your room from feeling stodgy.

3. Get a fan

Fans are by and large less expensive to run than air-con. Have one on the entire night to keep the air delicately moving. It can coax heat out of the room and even push it out the open window.

Get inventive. Put a bowl of ice shapes before the fan. The breeze will gradually drift the softening cold fume from the outer layer of the ice, creating a delightful, cooling fog.

4. Hydrate

Drink a glass of chilled water before bed to get your body hydrated and cool, and recharge water misfortune because of perspiring.

5. Have a warm shower before bed 4

On the off chance that you're feeling hot prior to making a beeline for bed, have a warm shower. Why not have a chilly one? Since your body will capture your endeavors by rapidly diminishing blood stream to your skin. A couple of moments some other time when the blood stream fires up once more, you'll feel hot once more. A warm shower will increment blood stream to your skin and increment heat misfortune from your body. Then you can slip between the sheets feeling spotless and agreeable.

6. Rest on ice

Ice, truly? Indeed! In the event that you're battling with heat, snatch an ice pack from the cooler, enclose it by a tea towel and spot it in the bed any place it feels great. Or on the other hand recover your high temp water bottle. Fill it with water and pop it in the cooler for a bed-accommodating arrangement.

For more moment help, put an ice pack on the beat focuses on your wrists, neck, elbows, crotch, lower legs and, surprisingly, behind your knees. The virus will travel rapidly around your body, and you'll see the distinction very quickly. Simply don't get excessively cold!

7. A moist pack

A blast from the past to assist your body with shedding a few additional degrees around evening time is to dampen a towel or material basically. Put it on your temple or body. Simply don't immerse the towel. You would rather not douse your sleeping pad and sheets!
Might it be said that you are experiencing continuous rest difficulties? Take free rest evaluation rest evaluation rest wellbeing

8. Store those covers

While covers and a doona are perfect during the colder evenings, keeping them on the bed just without much forethought can make you sweat over the course of the evening. This can upset your rest as your body battles to decrease its temperature. Once more, store them in a cabinet until it chills off.

9. Utilize breathable bed cloth

Lightweight, great quality bed cloth is breathable which implies that it won't trap your body heat. The less intensity that gets caught underneath your sheets, the simpler it is to feel cool and agreeable as you float off to rest.

So save the polyester, silk and glossy silk sheets for colder evenings or extraordinary events. Attempt cotton, material or bamboo filaments all things being equal!

10. Wear free cotton nightwear

Free, delicate cotton night wear can assist with keeping you cooler by dispersing the intensity, very much like cotton sheets do. They consider wind current and breathability, while engrossing abundance sweat from your skin.

The new English Premier League season 2022

The Premier League will have a number of new features for the 2022-23 season

The competition is widely believed to be the most-watched soccer league in the world

World Cup break
Given that the World Cup will take place in November and December in Qatar,  So the league will take an extended winter break from November 13 to December 26.

Extra substitutions
Teams will also be able to make up to five substitutions in every game, up from three previously allowed.

All change for referees
Some of the Premier League's most experienced referees, all in their 50s with a combined 63 years of top-flight experience, hung up their whistles in the summer.

Major transfers
Erling Haaland – Borussia Dortmund to Manchester CityDarwin Nunez – Benfica to LiverpoolRicharlison – Everton to TottenhamGabriel Jesus – Manchester City to ArsenalRaheem Sterling – Manchester City to Chelsea
Premier League exits
Sadio ManeAlexandre LacazettePaul PogbaRomelu LukakuAntonio RudigerAndreas ChristensenRaphinha Belloli

Promoted teams
FulhamBournemouthNottingham Forest

Taking a knee
Premier League teams will limit their pre-match anti-racism gesture of “taking the knee” to only some significant games from the new season

Opening-round fixtures
FridayCrystal Palace vs Arsenal

SaturdayFulham vs Liverpool

Bournemouth vs Aston Villa

Leeds United vs Wolverhampton Wanderers

Newcastle United vs Nottingham Forest

Tottenham Hotspur vs Southampton

Everton vs Chelsea
SundayLeicester City vs Brentford

Manchester United vs Brighton

West Ham vs Manchester City

How long is the Premier League season?
The Premier League season began Friday afternoon with Arsenal’s win at Crystal Palace and ends with a final Sunday of matches on May 28, 2023.

How can I watch the Premier League in the UK?
People located in the UK can watch Premier League matches at home through a legitimate subscription to one or all of the Premier League's authorised UK broadcasters, Sky Sports, BT Sport and Amazon Prime Video.

Scientific Financial Tips

Scientific Financial Tips:

When you think of science, what comes to mind? Atoms, technological advancements, the space-time continuum. These are all common attributions to the word science, but what about money?

What is science behind finance, investment and managment?

1. Brain, decision making and finance managment

2. Money and Mental Health

3. Investment is about risk and return or about science?


Artificial intelligence and its application

What is AI?

Artificial intelligence (AI), the ability of a digital computer or computer-controlled robot to perform tasks commonly associated with intelligent beings.

Application of artificial intelligence

  1. AI in healthcare
  2. AI in drug discovery
  3. Application in finance
  4. Applications Of Artificial Intelligence in Education
  5. Applications of Artificial intelligence in Navigation
  6. Applications of Artificial Intelligence in Robotics
  7. Applications of Artificial Intelligence in Agriculture
  8. Applications of Artificial Intelligence in Gaming
  9. Applications of Artificial Intelligence in Automobiles
  10. Applications of Artificial Intelligence in Social Media
  11. Applications of Artificial Intelligence in Marketing

1. Artificial intelligene in healthcare: Big data and machine learning are having an impact on most aspects of modern life, from entertainment, commerce, and healthcare. The healthcare ecosystem is realizing the importance of AI-powered tools in the next-generation healthcare technology. It is believed that AI can bring improvements to any process within healthcare operation and delivery. For instance, the cost savings that AI can bring to the healthcare system is an important driver for implementation of AI applications.

2. Artificial intelligene in Drug discovery: Over the past few years, there has been a drastic increase in data digitalization in the pharmaceutical sector. Machine Learning or AI is not really new but over last few years, application of better methods have emerged and they have been successfully applied for drug discovery and development. Machine learning and deep learning algorithms have been implemented in several drug discovery processes such as peptide synthesis, structure-based virtual screening, ligand-based virtual screening, toxicity prediction, drug monitoring and release, pharmacophore modeling, quantitative structure-activity relationship, drug repositioning, polypharmacology, and physiochemical activity.

It can be applied in following fields:

  • Target identification
  • Lead optimization
  • Virtual chemical screening
  • Pharmacophore
  • Drug repurposing

3. Artificial intelligene in Finance:  Artificial Intelligence (AI) techniques are being increasingly deployed in finance, in areas such as asset management, algorithmic trading, credit underwriting or blockchain-based finance, enabled by the abundance of available data and by affordable computing capacity. Machine learning (ML) models use big data to learn and improve predictability and performance automatically through experience and data, without being programmed to do so by humans. 

It can be used in following areas:

  • Trading
  • Risk managment
  • Risk assessment
  • Fraud detection, management and prevention
  • Managing finances/personalized banking
  • Better predict and assess loan risks
  • Save money
  • Credit Decisions
  • Process Automation
  • Fraud Prevention

Challenges of AI in Finance:

There are several challenges of AI in finance for example data quality, Biased data, Dimensionality reduction etc

Applications Of Artificial Intelligence in Education


Data Analysis, Interpretation and Visualization

What is data science?

Data science is the scientific study of data to gain knowledge. It is a multidisciplinary approach to extracting actionable insights from the large and ever-increasing volumes of data collected and created by today’s organizations. Data science encompasses preparing data for analysis and processing, performing advanced data analysis, and presenting the results to reveal patterns and enable stakeholders to draw informed conclusions.

What is Data analysis?

How to interpret your data?

How to visualize data?

Data science pipeline:

Data science tools: he most popular programming languages among data scientists are open source tools that include or support pre-built statistical, machine learning and graphics capabilities. These languages include: