sequenza on hg38?

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Christoffer Flensburg

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Nov 22, 2017, 12:02:06 AM11/22/17
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Hey all,

Does sequenza support hg38? The error message "Error : assembly must be one of hg19, hg18, hg17 or hg16" seems to indicate that it doesn't.

cheers,
/Christoffer

Francesco Favero

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Nov 22, 2017, 4:28:46 PM11/22/17
to Christoffer Flensburg, Sequenza User Group
Hi Christoffer,

sequenza per-se doesn’t really deal with genome build, the problem is in the copynumber package used for the segmentation.

here you can find how to use a modified version of copynumber to enable hg38, or any other genome build:
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Christoffer Flensburg

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Nov 22, 2017, 11:48:52 PM11/22/17
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Hey Francesco,

Thanks. I replaced library(sequenza) with

library(sequenza)
library("devtools")
install_github("aroneklund/copynumber")

which makes it pass that point of the run with hg38.

cheers,
/Christoffer
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Phoebe He

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May 15, 2019, 1:45:29 PM5/15/19
to Sequenza User Group
Hi Francesco,

It would be really nice if sequenza can be used for mouse genomes.  Is there a way to install copynumber for mm10 just like Christoffer did?

Thanks!
Phoebe

Christoffer Flensburg

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Oct 3, 2019, 9:59:27 PM10/3/19
to Sequenza User Group
Hi again Francesco!

I am back to running some Sequenza on hg38 again, and it seems there is an issue with the modified copynumber package. :/
in sequenza.extract, I get this error for each chromosome (GC information seems to go through properly).

Processing chr1:
Error in get0(oNam, envir = ns) :
  lazy-load database '/stornext/HPCScratch/home/flensburg.c/software/R/libs/copynumber/R/copynumber.rdb' is corrupt

I reinstalled the copynumber package, but the same error. I see that the github hasn't been touched for 3 years, but maybe some changes to R (this is version 3.6.0) or sequenza (3.0.0) has affected things?
Any ideas? Or are there now other ways to run Sequenza on hg38?

cheers,
/Christoffer

On Thursday, November 23, 2017 at 8:28:46 AM UTC+11, Francesco Favero wrote:
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Shixiang Wang

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Dec 2, 2019, 1:30:21 AM12/2/19
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I have the same issue and I created a fork from v1.26.0 https://github.com/ShixiangWang/copynumber, I hope it may help.

在 2019年10月4日星期五 UTC+8上午9:59:27,Christoffer Flensburg写道:

Natalia M

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Oct 27, 2020, 4:42:33 PM10/27/20
to Sequenza User Group
Hello!
Has anyone been successful in running Sequenza with samples aligned with GRCh38 -Ensembl version-?
Thanks!
Natalie

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Interestingly, the compound is structurally similar to serotonin—a neurotransmitter in your brain that regulates mood, sleep, and perception. For instance, Indigenous communities in South America have used DMT for centuries as part of ayahuasca ceremonies.
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Today, DMT exists in two main forms: natural extracts and synthetic versions made in laboratories. Street names for DMT include Dimitri, businessman’s special, and elf spice. The synthetic form typically appears as a white or yellowish crystalline powder.
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DMT vape pens work by heating the substance to a specific temperature where it vaporizes without combusting.
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The DMT experience is often described as unlike anything else in the world of psychedelic drugs. Within seconds of inhaling, users report entering completely altered states of consciousness that feel more real than everyday reality.
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Two of the defining characteristics of DMT are how quickly it works and how relatively short the effects last. Interestingly, that’s why some people nicknamed it “businessman’s special.” The entire experience can happen during a lunch break.
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To put the numbers in perspective: An LSD trip can last from 8 to 12 hours. Psilocybin experiences take from 4 to 6 hours. Finally, ayahuasca, which also contains DMT, produces effects lasting several hours.
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Seizures in rare cases, especially when mixing DMT with other substances (i.e., opioids or certain medications)

Psychological side effects include:

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Intense paranoia or frightening hallucinations that feel threatening

Overwhelming altered states that can feel inescapable

Risk of triggering or worsening existing mental health conditions

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What Are the Long-Term Effects of Using DMT?

The National Institute on Drug Abuse continues researching psychedelic substances, and evidence suggests DMT can have lasting impacts on mental health.
Common long-term effects include:

Flashbacks: Spontaneous re-experiences of the DMT trip that can happen days, weeks, months, or even years after use.

Visual distortions: Sudden episodes where you see patterns or colors even when sober.

Trigger sensitivity: Flashback episodes triggered by stress, fatigue, physical exercise, or use of other substances.

Worsening of pre-existing conditions: Intensified symptoms for those with a history of anxiety, depression, or psychosis.

Cardiovascular effects: DMT consistently raises blood pressure and heart rate during use, and repeated use can potentially impact heart health over time.

Unpredictable mental health impacts: The relationship between DMT and long-term psychological well-being remains under study.

Unlike many controlled substances, DMT doesn’t appear to cause physical withdrawal symptoms or traditional addiction patterns. However, the lack of physical dependence doesn’t mean the substance is safe or without serious health issues.
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What Makes DMT Vape Pens Dangerous?

DMT vape pens have unpredictable potency. Unlike pharmaceutical medications with standardized doses, street DMT varies wildly in strength. One cartridge might be relatively weak while another can be overwhelmingly powerful.
Quality and purity are other concerns. You have no way of knowing what else might be in a DMT vape cartridge that you illegally purchase. Contaminants, cutting agents, or other psychedelic substances could be mixed in without your knowledge.
Mixing DMT with other substances dramatically increases risks. If anything, combining it with LSD, psilocybin, or opioids can trigger serotonin syndrome. The latter is a potentially life-threatening condition.
Finally, the convenience of vape pens might encourage more frequent use. As a result, it increases your exposure to both short-term and long-term health issues.
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Get Help for DMT Use Today

DMT vape pens might seem like a quick path to profound experiences, but the risks to your mental health, physical safety, and future don’t make it worth experiencing. Experimenting is one thing, but problematic use requires intervention.
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Published on: 2025-12-30
Updated on: 2026-01-16

Posted in Hallucinogens

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When it comes to Fryd Extracts, distinguishing real from fake is essential for your safety and satisfaction. Always purchase from authorized retailers, check for lab test results, and scrutinize the packaging. Protect yourself from counterfeit products and enjoy the premium experience that Fryd Extracts promises.

By staying informed and vigilant, you can confidently answer the question, "Fryd Extracts real or fake?" and make the best choice for your cannabis needs. fryd extracts real or fake

Fryd Carts Wholesale
Fryd Carts Wholesale. If you are someone who is always on the move and has a busy lifestyle, then you know how important it is to have a reliable vape device that you can take with you anywhere. Look no further than  Fryd Disposable Vapes! These compact, lightweight, and easy-to-use devices are perfect for on-the-go vaping and offer a range of delicious flavors to choose from. Whether commuting to work, traveling, or running errands, Fryd Disposable Vapes provide a hassle-free vaping experience that can be enjoyed anytime, anywhere.

In this blog post, we’ll dive into the features and benefits of Fryd Disposable Vapes and explore why they are the perfect choice for anyone who is always on the move. So, sit back, relax, and let’s explore why Fryd Disposable Vapes are the ultimate on-the-go vaping companion. fryd extracts real or fake

Advantages of Fryd Disposable Vapes
Disposable vapes are the ultimate solution for those who desire an easy and convenient vaping experience. With their pre-filled nature, users can enjoy them straight out of the box without worrying about refilling . Each Fryd disposable vape is packed with a rich and satisfying flavor that is sure to leave vapers wanting more. All  disposables vapes are made using high-quality ingredients, including Fryd extract, which provides an authentic  taste .

Whether you’re a vaping enthusiast or a casual user looking for an easy-to-use device, Fryd disposable vapes are the perfect choice. With a wide selection of flavors to choose from, you’re sure to find one that suits your personal taste and preference. Try a Fryd disposable vape today and experience its convenience and satisfaction!

Fryd Carts – fryd extracts real or fake
Fryd 2g disposables offer a unique and convenient vaping experience that users are sure to love. Fryd carts bulk sale, Not only are they compact and easy to carry around. This means that users no longer have to worry about buying multiple juices or pods. Fryd  provide a hassle-free vaping solution for those always on the go. The disposable nature of Fryd 2g ensures that users can easily switch between their favorite flavors. So, why not try out Fryd disposables today and discover the convenience of a hassle-free vaping experience? fryd extracts real or fake

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Meanwhile, Fryd disposable vapes offer a unique vaping experience that is unrivaled by other e-cigarettes on the market. These devices are incredibly convenient, affordable, and discreet. They don’t require any complicated maintenance procedures and can easily fit in your pocket or purse, allowing you to take your favorite flavors with you wherever you go. Fryd carts bulk sale, if  you’re looking for a discreet and hassle-free vaping experience or simply want to try something new, Fryd vapes are the perfect solution. So, if you want to enjoy the  vape with rich flavors of your favorite dessert, this is  worth checking out. Fryd extracts real or fake

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For anyone leading a busy and active lifestyle, this vaping device is perfect. Thanks to its slender and sleek design, it can fit into any pocket or purse, enabling you to access your vape anytime and anywhere. Unmatched in affordability and convenience, this device requires no charging or maintenance. The disposable charger provides an even more convenient option, allowing users to charge their devices on the go.

Regardless of whether you're running errands or traveling, the Fryd Dispo has got you covered. With its simple operation and hassle-free use, Fryd vapes enable you to enjoy your favorite vaping experience with ease. So why wait? Take your vaping experience to the next level by purchasing your Fryd Dispo today. fryd extracts real or fake

On Wednesday, November 22, 2017 at 6:02:06 AM UTC+1 Christoffer Flensburg wrote:
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