Tag: SAM

UMI workflow resulting in bams with empty reads

Hello all, In my NGS workflow for UMI based reads, I first tried identifying and removing sequence adapters using bbmerge and cutcadapt: BBMERGE -Xmx1g -ignorejunk in1=SAMPLE_R1 in2=SAMPLE_R2 outa= adapters.fa itn CUTADAPT -a forward_adapter -A reverse_adapter -o s_2_1_sequence_trimmed_UN.fastq.gz -p s_2_2_sequence_trimmed_UN.fastq.gz SAMPLE_R1 SAMPLE_R2 Then, I converted the trimmed fastq files to an…

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Ubuntu Manpage: samtools-quickcheck – a rapid sanity check on input files

Provided by: samtools_1.19-1_amd64 NAME samtools-quickcheck – a rapid sanity check on input files SYNOPSIS samtools quickcheck [options] in.sam|in.bam|in.cram [ … ] DESCRIPTION Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and…

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Ubuntu Manpage: FastQC – high throughput sequence QC analysis tool

Provided by: fastqc_0.11.9+dfsg-5_all NAME FastQC – high throughput sequence QC analysis tool SYNOPSIS fastqc seqfile1 seqfile2 .. seqfileN fastqc [-o output dir] [–(no)extract] [-f fastq|bam|sam] [-c contaminant file] seqfile1 .. seqfileN DESCRIPTION FastQC reads a set of sequence files and produces from each one a quality control report consisting of…

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PRSice and R lm() show different association analysis output (coefficient, SE and P)

PRSice and R lm() show different association analysis output (coefficient, SE and P) 0 Hey, I am struggling to understand Why am I getting different association analysis output (coefficient, SE and P) between PRSice and lm() function in R. Not only the values, even the direction of association is different….

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sam file error

sam file error 1 Hi, I was converting my sam file (after alignment with bowtie2) in bam format. I encountered the error: [E::sam_parse1] invalid QUAL character [W::sam_read1_sam] Parse error at line 11129453 command: samtools view -S -b -o input.bam ../alignment/input.sam Alignment works fine. This is the output: 22504890 reads; of…

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Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals

The specific environmental/history/collection context The Huseby Klev materials were unearthed and collected by archaeologists (including two of the co-authors of this article) during the excavation of this coastal hunter-fisher-gatherer site in the 90s50. The material assemblage was rich and well preserved: human bones, animal bones, plant remains and pieces of…

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BWA Index Referencing Failed. Possible Reason and Solutions?

BWA Index Referencing Failed. Possible Reason and Solutions? 0 Script: echo “STEP 2: Map to reference using BWA-MEM” #BWA index reference bwa index ${ref} *#Path for ref variable has been defined* #BWA alignment bwa mem -t 4 -R “@RG\tID:SRR062634\tPL:ILLUMINA\tSM:SRR062634” ${ref} ${reads}/SRR062634_1.filt.fastq.gz ${reads}/SRR062634_2.filt.fastq.gz > ${aligned_reads}/SRR062634.paired.sam **Error:** . . . . [BWTIncConstructFromPacked]…

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Crispr Library Download

CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared…

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java -jar picard.jar manual | BioQueue Encyclopedia

Category Sam/Bam Manipulation Usage java -jar picard.jar SetNmMDAndUqTags I=sorted.bam O=fixed.bam \ Manual INPUT (File)    The BAM or SAM file to fix. Required. OUTPUT (File)    The fixed BAM or SAM output file. Required. IS_BISULFITE_SEQUENCE (Boolean)    Whether the file contains bisulfite sequence (used when calculating the NM tag). Default value: false. This option can be…

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Secretsdump Download

We transfer the hive files onto our Kali Linux Machine, to extract hashes from them. We will be using the secretsdump.py file from the impacket toolkit to extract hashes. All we need is to provide the path of the SYSTEM hive file and the NTDS.dit file and we are good…

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Year in review: Generative AI takes the tech world by storm

To say 2023 was a year taken up mostly by AI would be a massive understatement. Following the release of ChatGPT at the very end of 2022, generative AI blew up in 2023.  According to Reuters, ChatGPT had grown to 100 million active users by January 2023, which was just…

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Sacramento bee obituaries for today

Sacramento,CA Obituaries. The Dignity Memorial® online obituary search tool gives you access to obituaries from thousands of locations across North America. You can search by first or last name, state and publication date. Once you find the obituary you are looking for, you can get important information about upcoming services,…

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Old convertible cars for sale near me

Catalytic converters are an important part of a car’s emission system, and they can be recycled for scrap metal. Selling catalytic converter scrap can be a lucrative business, but there are a few things to consider in order to maximize prof…1968 Oldsmobile 442 Beautiful Vintage Convertible! 75,894km Specs: Engine Size…

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Human CD26 (DPP4) activation kit by CRISPRa Clinisciences

Kit Components GA101256G1, CD26 gRNA vector 1 in pCas-Guide-GFP-CRISPRa, Target Sequence: CGACGTCATTTTTAGCTAAG GA101256G2, CD26 gRNA vector 2 in pCas-Guide-GFP-CRISPRa, Target Sequence: GAGCCGTGGGGGAGGGGAAA GA101256G3, CD26 gRNA vector 3 in pCas-Guide-GFP-CRISPRa, Target Sequence: AACCTCACGTGGACAGGCGA 1 CRISPRa-Enhancer vector, SKU GE100056 1 CRISPRa scramble vector, SKU GE100077 Disclaimer These products are manufactured and supplied…

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Error in schicexplorer’s hicbuildmatrix

Error in schicexplorer’s hicbuildmatrix 1 I use schicexplorer’s hicbuildmatrix code; it complains that two sam files do not have the same reads order hicbuildmatrix schic • 801 views My best guess at the moment is that you need R1 and R2 bam files sorted by read name, not the default…

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AI Week In Review 23.12.16

Figure 1. Tesla’s Optimus Gen2 demo video, showing off tactile precision. Midjourney Alpha web interface is available here to super-users who generated over 10k Midjourney images. This will be a big UX upgrade for Midjourney users over the discord text prompt method. Google has released Imagen2 text-to-image generation for Vertex…

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Human TIA1 activation kit by CRISPRa Clinisciences

Product Data Format 3 gRNAs (5ug each), 1 scramble ctrl (10ug) and 1 enhancer vector (10ug) Symbol TIA1 Locus ID 7072 Kit Components GA104875G1, TIA1 gRNA vector 1 in pCas-Guide-GFP-CRISPRa GA104875G2, TIA1 gRNA vector 2 in pCas-Guide-GFP-CRISPRa GA104875G3, TIA1 gRNA vector 3 in pCas-Guide-GFP-CRISPRa 1 CRISPRa-Enhancer vector, SKU GE100056 1…

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An FGFR2 mutation as the potential cause of a new phenotype including early-onset osteoporosis and bone fractures: a case report | BMC Medical Genomics

Anamnesis vitae A 13 year old male born was as result of the VII pregnancy, from unrelated parents. Other pregnancies resulted in: I-II silent miscarriage in the second trimester; III – female, born in 2003 (III-3 Fig. 1) that has the following phenotypic features: genu valgum, hip dysplasia, combined thoracolumbar scoliosis,…

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r – looping over several columns to create ggplots

You must adapt the function to have the column names as argument, not the column vectors. The code comments explain how it is made. Then loop over names(df2). suppressPackageStartupMessages( library(tidyverse) ) # Create Vectors var1 <- c(‘A’,’A’,’B’,’B’) var2 <- c(1,2,2,1) var3 <- c(‘sam’,’sam’,’saul’,’saul’) # Create DataFrame df <- data.frame(var1,var2,var3) #…

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14 predictions about 2024

“The numerals 2024 set against a futuristic, utopian cityscape” / DALL-E A year ago, as I sat down to write my predictions for 2023, two things seemed unusually clear. One was that Elon Musk’s purchase of Twitter was disrupting the old order in social networking far faster and more dramatically…

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Research on 3D Instance Segmentation part1(Artificial Intelligence Fall ‘23) | by Monodeep Mukherjee | Dec, 2023

SAM-guided Graph Cut for 3D Instance Segmentation(arXiv) Author : Haoyu Guo, He Zhu, Sida Peng, Yuang Wang, Yujun Shen, Ruizhen Hu, Xiaowei Zhou Abstract : This paper addresses the challenge of 3D instance segmentation by simultaneously leveraging 3D geometric and multi-view image information. Many previous works have applied deep learning…

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Lightning AI Unveils Lightning AI Studios to Advance the AI Development Landscape

NEW YORK, Dec. 13, 2023 — Lightning AI, the company behind PyTorch Lightning, with over 91 million downloads, today announced the introduction of Lightning AI Studios, the culmination of three years of research into the next-generation development paradigm for the age of AI. Software 1.0 such as web apps, servers, etc.,…

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Lightning AI, creator of PyTorch Lightning framework, debuts platform for building and deploying AI apps

Lightning AI Inc., the company behind the popular artificial intelligence development framework PyTorch Lightning, is evolving its offerings with the launch of Lightning AI Studios with a goal to simplify the way enterprises can build and deploy AI-infused applications. Announced today, the new offering delivers a more comprehensive, intuitive and…

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Lightning AI Introduces Lightning AI Studios; its Enterprise-Grade Platform for Rapid-prototyping, and Deploying AI Products

Article content The ‘Operating System’ for AI Development; Lightning AI Studios is The Enterprise-Grade Platform that Allows AI Developers to Code on Cloud GPUs from the Browser or their Laptops with Zero Setup NEW YORK — Lightning AI, the company behind PyTorch Lightning, with over 91 million downloads, today announced…

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What is Gemini? Google’s AI model and GPT-4 alternative explained

Key Takeaways Gemini is Google’s new multimodal AI model that can take in text, images, videos, and sound, and produce output in any of those formats. Gemini outperforms human experts and OpenAI’s GPT-4 on language understanding benchmarks, making it a powerful generative AI model. Gemini is already being used in…

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Circulating Tumor DNA Monitors Hodgkin Lymphoma Prognosis

A Stanford Medicine-led, international study of hundreds of samples from patients with Hodgkin lymphoma has shown that levels of tumor DNA circulating in their blood can identify who is responding well to treatment and others who are likely to experience a disease recurrence — potentially letting some patients who are…

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Hodgkin lymphoma prognosis, biology tracked with circulating tumor DNA | News Center

A Stanford Medicine-led, international study of hundreds of samples from patients with Hodgkin lymphoma has shown that levels of tumor DNA circulating in their blood can identify who is responding well to treatment and others who are likely to experience a disease recurrence — potentially letting some patients who are predicted…

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Big money investments, not acquisitions, fuel GenAI startups

The rapid growth of generative AI technology has quietly but dramatically reduced the number of AI acquisitions while creating a new investment strategy by the tech giants. Throughout 2023, tech giants Microsoft, Google and AWS have steadily released GenAI applications, including Microsoft incorporating the technology into its Bing search…

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Liquid Biopsy Uses ctDNA to Predict Recurrence of Hodgkin Lymphoma

A Stanford Medicine-led, international study of hundreds of samples from patients with classic Hodgkin lymphoma (cHL) has shown that levels of tumor DNA circulating in the blood can identify those individuals who are responding well to treatment and those who are likely to experience a disease recurrence. The study results suggest…

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Rating the Cloud Wars Top 10 CEOs –

With the combined market cap of the Cloud Wars Top 10 companies now exceeding $7 trillion — and take a moment to wrap your noggin around that — it would be easy to assume the CEOs of those world-shaping companies all delivered superb performances in 2023. But is that in…

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Insert Size For Illumina Gaiix Paired-End Library From Sam/Bam File

Insert Size For Illumina Gaiix Paired-End Library From Sam/Bam File 2 From the fastq data (read 1 and read 2) from illumina GAIIx platform ( paired-end library), I created the Sam and bam file using BWA. I got the statistics of number of uniquely-paired reads and total reads mapped to…

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r – Fst calculation from VCF files

I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and SNPs_s4.vcf, which contain information about SNPs. These vcf files were obtained by using the following methods: the initial input files were short-paired reads I did mapping with minimap2 ./minimap2 -ax sr ref.fa read1.fq.gz read2.fq.gz > aln.sam converted to bam file samtools…

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Ada Nicodemou shows off her trim pins in glistening frock as she leads the arrivals at Channel Seven Christmas bash alongside Sam Mac

By Marta Jary For Daily Mail Australia Published: 06:56 GMT, 9 December 2023 | Updated: 11:01 GMT, 9 December 2023 Ada Nicodemou was ready for a festive good time on Saturday night.  The Home and Away star was among the celebrities heading in to the Channel Seven Christmas bash in Sydney. …

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Effects of diabetes mellitus and glycemic traits on cardiovascular morpho-functional phenotypes | Cardiovascular Diabetology

American Diabetes A. Economic costs of Diabetes in the U.S. in 2017. Diabetes Care. 2018;41(5):917–28. Article  Google Scholar  Linssen PBC, Veugen MGJ, Henry RMA, van der Kallen CJH, Kroon AA, Schram MT, Brunner-La Rocca HP, Stehouwer CDA. Associations of (pre)Diabetes with right ventricular and atrial structure and function: the Maastricht…

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Sunder Pichai’s Demo Of Google’s Most Powerful AI ‘Gemini’ Impresses Elon Musk

Based on their designs, which of these models will go faster? How do you think a computer would answer in real time? Here’s how Google’s latest AI model, Gemini 1.0, answered in a blink of an eye. And wait, it can do much more, but here’s a glimpse of some…

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sam – Discrepancy in Read Counts Between FastQ and BAM Files in Adapter-Trimmed Pipeline

In a FastQ to BAM pipeline where only adapter trimming is performed, I’ve noticed a potential discrepancy in read counts between the initial FastQ files and their resulting BAM file. Specifically, I’m seeking clarification on whether the following statement holds true: “Total number of reads in R1 and R2 FastQ…

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AI Bots Experience ‘Hallucinations’ as Google Launches Gemini AI Model

On Wednesday, Google launched its new artificial intelligence model, which is considered its largest and most capable. The language model, called Gemini, will feature three different sizes: Gemini Ultra, its most significant, most capable category; Gemini Pro, which ranges over a wide variety of tasks; and Gemini Nano, which it…

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Google DeepMind Unveils Gemini, Its Most Powerful AI Offering Yet

Google DeepMind has announced its much-anticipated family of artificial intelligence chatbots, Gemini, which will compete with OpenAI’s GPT series. According to Google, Gemini Ultra, its largest and most capable new model, outperforms OpenAI’s most capable model, GPT-4, at a number of text-based, image-based, coding, and reasoning tasks. Gemini Ultra will…

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Large-scale DNA sequence resource reveals new regions of the human genome under natural selection

BOSTON – Every human’s genome has millions of genetic variants, but most have little to no effect, making it difficult for clinicians to make medical diagnoses based on genetic differences. Using patterns of variation from tens of thousands of individuals with whole-genome sequence data, a team led by investigators at…

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Google Gemini AI launched! Set to take on OpenAI’s ChatGPT. Big boost for Bard, Pixel 8 Pro users

After delaying the launch just a few days ago and indicating that it would see the light of day sometime early next year, Google Gemini AI has finally, been rolled out! Google, the ‘AI first’ company is finally fighting back against OpenAI’s ChatGPT about a year after the latter’s launch….

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How To Install bedtools on Debian 11

In this tutorial we learn how to install bedtools on Debian 11. bedtools is suite of utilities for comparing genomic features Introduction In this tutorial we learn how to install bedtools on Debian 11. What is bedtools bedtools is: The BEDTools utilities allow one to address common genomics tasks such…

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Sorted bam files are empty after sorting them from bam

Sorted bam files are empty after sorting them from bam 0 Hi, I have been working with all my DNA analysis files in parallels but I got to a point where I had about 15 files get stuck on one step. Specifically, I notice something is wrong because the files…

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Bold Predictions for Generative AI in 2024

As we are nearing the end of 2023, we are probably standing at the high crest of the generative AI wave. From being termed word of the year to being the crux of every major big tech company announcements this year, including Google, Microsoft, and others, it is a no-brainer…

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Congressmen, industry leaders call on EPA to finalize emissions rule

© Shutterstock On Wednesday, U.S. Sens. Alex Padilla (D-CA) and Sheldon Whitehouse (D-RI) joined leaders from the heavy-duty vehicle industry to urge the Environmental Protection Agency (EPA) to finalize emission rules. The Senators, along with Matt LeDucq, CEO of Forum Mobility; Nikolas Runge, CTO of InCharge; Nate Baguio, senior vice…

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Google Gemini To Arrive Sooner Than Expected

According to reports, Google has delayed the launch of Gemini until January, just one month away. This is after announcing the AI at the Google I/O 2023, the company had postponed the launch of Gemini to the first quarter of next year, and Sundar Pichai has scrapped a series of…

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How to Regulate Unsecured “Open-Source” AI: No Exemptions

Wes Cockx & Google DeepMind / Better Images of AI / AI large language models / CC-BY 4.0 Unsecured “open-source” AI systems pose a massive series of threats to society and democracy. They deserve no exemptions and should be regulated just like other high-risk AI systems. Their developers and deployers…

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ida – Need help when reading .sam file of cocos2D game

so recently I tried to reverse a dead game apk to get their animation cause it’s so unique that me and my friend want to remake it. But it took so long to just take each part of the image and combine it to get a frame of an animation….

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Yes .. BBMap can do that!

NOTE: This collection was originally posted at SeqAnswers.com. Creating a copy here to preserve the information.Part I is available here: Yes .. BBMap can do that! – Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)Part II is available here: Yes .. BBMap can…

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Telethon Kids Institute hiring Bioinformatics Engineer in Perth, Western Australia, Australia

The Opportunity We are seeking a highly skilled and motivated Bioinformatics Engineer to join our Indigenous Genomics team, here at the Telethon Kids Institute. The Indigenous Genomics team operates out of Perth, Adelaide and Melbourne, and comprises a diverse, multi-disciplinary, Indigenous-led group of professionals and researchers, with expertise across genomics,…

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Extracting only soft/hard clipped reads from a bam file

Extracting only soft/hard clipped reads from a bam file 4 Hello all! I am working on some data but need a little bit of help with a bit of an unusual task. We are looking at where lentiviral DNA has inserted itself in our host genome, and to do this…

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filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts

filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts 0 hi folks, apologies if this has been answered elsewhere. I’m using read mapping to quantitate the abundance of viral metagenome assembled genomes (MAGs) across samples and I’d like to do a bit of data cleaning that’s…

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There are 1 region(s)/phenotype(s) with p-value > 0.1 (not significant).

I’m trying to get a PRS for a very small subset of samples (~400 training, ~200 testing). Firstly I C+T the training data previous to PRSice. My .log is PRSice 2.3.3 (2020-08-05) github.com/choishingwan/PRSice(C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O’ReillyGNU General Public License v3If you use PRSice in…

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Population-specific distribution of TPMT deficiency variants

Introduction Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes the S-methylation of purine analogs, including azathioprine, 6-mercaptopurine (6-MP), and thioguanine.1 The metabolism of these drugs results in two types of metabolites: S-methylmercaptopurine and S-methylthioguanine, which are generally described as inactive metabolites, and S-methyl-thioinosine monophosphate, an inhibitor of de novo…

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Effect allele flipping

Dear Sam and all, I used PRSice for calculating PRS based on the well-known 30 SNP list that is specific for type 1 diabets. I found that PRSice version 2.6.1 considered only SNPs whose effect allele are alternative alleles in the target file for PRS calculation. All SNPs that thier…

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bwa mem hangs after a few thousand reads

I am trying to align a bunch of paired sample fastq files using bwa mem. My original command was: bwa mem -t 8 hg38.fa sample_read1.fq.gz sample_read2.fq.gz > sample_paired.sam I am running this on a HPC cluster. These files have approx. 25 million reads, so I initially anticipated that they might…

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How to get unaligned reads and aligned reads into separate files from SAM/BAM?

How to get unaligned reads and aligned reads into separate files from SAM/BAM? 0 I have long reads aligned with MiniMap2 in the form of SAM file. I want to get my unmapped reads into a file called unmapped.fastq.gz and my aligned reads into a file called mapped.fastq.gz. How can…

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Bowtie mapping for single_end read

Bowtie mapping for single_end read 1 bowtie –threads 5 -X 1000 -m 1 -v 2 –best –strata –sam IndexedGenome ${DATA_DIR}${SRR_ID}.trim.fastq > ${SAM_DIR}${SRR_ID}.sam Hi All, I am using the above script to map single_end ChIP-Seq reads. The percentage of the aligned reads is around 20%. How can I modify the script…

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I made an error when using metawrap to binning

I made an error when using metawrap to binning 1 my code metawrap binning -o bin_out -t 24 -m 200 -a all_contig/all_merge.fasta –metabat2 –maxbin2 –concoct all_fastq/*fastq Error reported as follows sorting the SRR10492802 alignment file [bam_sort_core] merging from 24 files and 24 in-memory blocks… [E::sam_hdr_sanitise] Malformed SAM header at line…

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Implementing Soft Nearest Neighbor Loss in PyTorch | by Abien Fred Agarap | Nov, 2023

Representation learning is the task of learning the most salient features in a given dataset by a deep neural network. It is usually an implicit task done in a supervised learning paradigm, and it is a crucial factor in the success of deep learning (Krizhevsky et al., 2012; He et…

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Python Tools for Genomic Data Analysis: From Sequences to Structures | by Bao Tram Duong | Nov, 2023

Analyzing genomic data, from sequences to structures, is a critical aspect of bioinformatics. Python has a rich ecosystem of tools and libraries specifically designed for genomic data analysis. Here’s an overview of key tools and libraries for various stages of genomic data analysis: Description: Biopython is a comprehensive open-source collection…

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Who will win the battle for AI in the cloud? Maybe everyone

The speed with which Microsoft Corp. hired former OpenAI LP Chief Executive Sam Altman last weekend, along with the firm’s co-founder and an unspecified number of technical specialists, illustrates how high the stakes are in the $60 billion market for cloud artificial intelligence products and services. Microsoft, which by all…

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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

journal contribution posted on 2023-11-23, 11:51 authored by Marc F Lensink, Guillaume Brysbaert, Nessim Raouraoua, Paul A Bates, Marco Giulini, Rodrigo V Honorato, Charlotte van Noort, Joao MC Teixeira, Alexandre MJJ Bonvin, Ren Kong, Hang Shi, Xufeng Lu, Shan Chang, Jian Liu, Zhiye Guo, Xiao Chen, Alex Morehead, Raj S…

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These doctors blamed the woman’s exhaustion on her weight

In a viral video, a woman shockingly revealed that her doctors blamed her weight for her severe fatigue and migraines. Read on for the full story. Article continues below ad In November 2023, TikTok creator Sam Hart (@thesam_show) took to the social media platform and dropped a major bombshell about…

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The OpenAI meltdown: Winners and losers in the battle for AI supremacy

Conventional wisdom says Microsoft Corp. is the big winner in the recent OpenAI saga. We don’t quite see it that way. Both Microsoft and OpenAI are in a worse position today than it was last Thursday, prior to the firing of OpenAI Chief Executive Sam Altman and the ongoing public…

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Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject

Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject 0 Hello, I’m trying to compare alignment results between mapping tools, however, I’ve noticed that the .sam files I’ve made using vg surject are missing the NM:i field. Is there a way to generate a…

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Structural analysis of the Sterile alpha motif (SAM) domain of the Arabidopsis mitochondrial tRNA import receptor

Abstract Mitochondria are membrane bound organelles of endosymbiotic origin with limited protein coding capacity. As a consequence, the continual import of nuclear-encoded protein and nucleic acids such as DNA and small non-coding RNA is required and essential for maintaining organelle mass, number and activity. As plant mitochondria do not encode…

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Unlocking the secrets of chimerism: Plastid g

The global indoor plant market is burgeoning, with projections of reaching $7.27 billion by 2025. Chimeric plants, first noted in the 17th century, have become popular for their distinctive variegated patterns. These patterns are a product of the structure and development of the plant’s shoot apical meristem (SAM). Recent studies…

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Record Store Day Guide To 14 Unreleased & Reissued Jazz Recordings: Brubeck, Evans, Jamal & More

Rather than provide our usual detailed reviews of these never-before-released and/or reissued jazz recordings, we will instead provide a summary of each in alphabetical order by artist. While we see some of the usual suspects such as Bill Evans, Wes Montgomery, Charles Mingus, and Oscar Peterson, we also see Les…

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Issues while running htseq-count

Issues while running htseq-count 0 My data is Candida glabrata and when i use htseq-count, no read is mapped to the gene_id. Thank you for your time and help. Foad htseq-count GSNO_SRR1582646.sam Candida_glabrata_genome.gtf > GSNO_SRR1582646.count 10975 GFF lines processed. 8843 alignment record pairs processed. head GSNO_SRR1582646.count gene-CAGL0A00165g 0 gene-CAGL0A00187g 0…

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Texas A&M Researchers Develop Comprehensive Genetic Map For Bison, Discover Gene Responsible For Albinism

White Cloud, a female albino bison, lived with the National Buffalo Museum herd in Jamestown, North Dakota, until her death in 2016 at the age of 20. Researchers at Texas A&M University’s School of Veterinary Medicine and Biomedical Sciences recently the discovered the gene responsible for albinism in bison. Photo…

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Sam Altman joins Microsoft to lead new “advanced AI research team”

Sam Altman is set to join Microsoft to lead a new AI research team following his abrupt departure from OpenAI, CEO Satya Nadella has announced.  In a statement online, Nadella revealed Altman and OpenAI’s former president, Greg Brockman, will join the firm to lead what he described as an “advanced…

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Qualimap bamqc v2.2.2 Cannot invoke “org.bioinfo.ngs.qc.qualimap.beans.XYVector.getXVector()” because “this.data” is null

That solves the problem! It is a panel data so I thought it would be expected not to have regions outside the given intervals. Maybe just for completeness, what are the implications of not supplying a –feature-file ?  Otherwise, the problem is resolved: “` QualiMap v.2.2.2-devBuilt on 2019-11-11 14:05 Selected…

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ChatGPT Maker’s CEO Talks AI at APEC Summit in San Francisco

The second day of the APEC CEO Summit was marked by last-minute cancellations of some of the highest-profile scheduled speakers. Chinese President Xi Jinping, set to give a talk Thursday morning, canceled at the last minute, instead offering a statement on the CEO Summit’s website. He was present at the…

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STAR output

STAR output 1 Hello, I am trying to map with STAR but it is not clear to me why I am not getting the SAM/BAM mapping file, could you help me? [epola@mazorka alignment_STAR]$ ls -lh total 13M -rw-rw-r– 1 epola epola 13M Nov 17 12:34 SRR22164928SJ.out.tab -rw——- 1 epola epola…

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Vertex Pharmaceuticals’ Casgevy Wins U.K. Approval for Sickle Cell Disease

In a landmark announcement for the CRISPR field and the sickle cell disease (SCD) community, the U.K. authorities have granted approval to Casgevy, the CRISPR-Cas9 therapy formerly known as exa-cel developed by Vertex Pharmaceuticals and CRISPR Therapeutics. The U.S. Food and Drug Administration (FDA) is expected to follow suit in…

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Microsoft unveils Maia 100 AI chip and Cobolt 100 CPU for Azure

Microsoft has unveiled its first custom silicon, launching two chips, the Maia 100 (M100) AI accelerator and the Cobolt 100 CPU, designed to handle artificial intelligence and general purpose workloads on its Azure cloud platform. Microsoft has unveiled two custom chips for its Azure Cloud platform. (Photo courtesy of Microsoft)…

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United States License Management Markets, Competition, Forecast & Opportunities, 2028F

Company Logo Dublin, Nov. 15, 2023 (GLOBE NEWSWIRE) — The “United States License Management Market, Competition, Forecast & Opportunities, 2018-2028” report has been added to ResearchAndMarkets.com‘s offering. The projected market size for the United States license management market was valued at USD 166.42 in 2022, and is expected to register…

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Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped

Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped 0 I am trying to extract unaligned reads from bam files and then realign them back to hg38. Here are the commands for these steps: samtools view -@ 16 -b -F 2 $bamfile | samtools…

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Bowtie2 Local Alignment Not Working

I have an amplicon library, which I am trying to align with bowtie2 but I am having issues. My reads have been trimmed to removed the 5′ and 3′ adapters, which ideally should result in 20bp trimmed reads. However, sometimes, there are reads that are 22-23bp. The indexes that I…

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samtools – Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped

I am trying to extract unaligned reads from bam files and then realign them back to hg38. Here are the commands for these steps: samtools view -@ 16 -b -F 2 $bamfile | samtools sort -@ 16 -n – | samtools fastq – -1 unaligned.fq1 -2 unaligned.fq2 bwa aln -k…

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Oncogenic activation revealed by FGFR2 genetic alterations in intrahepatic cholangiocarcinomas | Cell & Bioscience

Everhart JE, Ruhl CE. Burden of digestive diseases in the United States Part III: Liver, biliary tract, and pancreas. Gastroenterology. 2009;136(4):1134–44. Article  PubMed  Google Scholar  Khan SA, Thomas HC, Davidson BR, Taylor-Robinson SD. Cholangiocarcinoma. Lancet. 2005;366(9493):1303–14. Article  PubMed  Google Scholar  Nakanuma Y, Klimstra DS, Komuta M, Zen Y (2019) Intrahepatic…

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Astria Therapeutics shares Q3 results, positive phase 1a data, and pipeline expansion By Investing.com

© Reuters. Astria Therapeutics recently reported its third-quarter financial results and provided a corporate update, highlighting its promising Phase 1a data for STAR-0215, a potential preventative treatment for Hereditary Angioedema (HAE). The company also announced the expansion of its pipeline with STAR-0310, a potential therapy for atopic dermatitis. Key takeaways…

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Converting Bam To Fastq

Converting Bam To Fastq 5 Any suggestions on good programs or scripts to convert a BAM file back to a fastq? I have found some scripts but wanted to ask for advice before I go too far down the wrong path. next-gen-sequencing fastq • 40k views Use SamToFastq UPDATE 2023:…

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More Thoughts on Artificial Intelligence

I published Thoughts on Artificial Intelligence on 19 July 2023. Since then, developments in AI have continued at a breath-taking speed. In here, I want to share new thoughts on AI that I have, as well as provide updates on some of the initial discussions. Let’s start with the new thoughts, in…

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A dyeing art, buy vs. lease

Hi, Quartz members! Missed any of our other newsletters this week? Space Business looked at the lay of the land for US spaceports, The Memo from Quartz at Work shared the secret for sticking with long-term projects, and the Quartz Obsession had bushels of information about the global wheat trade….

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bwa-mem2 error: skip or orientatioon FF

bwa-mem2 error: skip or orientatioon FF 1 I am having some problems with using bwa-mem2 After using the command line(below): there is some error in my results. The error message stated: “Skip or orientation FR as there are not enough pairs. paired reads have different names. How can I solve…

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University of Alabama at Birmingham hiring BIOINFORMATICIAN I in Birmingham, Alabama, United States

Position Summary: The primary role is to execute a variety of data management and analysis tasks, ensuring the quality, reproducibility, and efficiency of processes related to high-dimensional data. You will collaborate with study investigators and fellow bioinformatics professionals within the department to contribute to high-quality, reproducible research across various scientific…

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Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance

Sample collection and spiking Chicken fecal samples were collected and processed as follows: one spoonful of fecal material (≈ 1 g) was collected and stored in a DNA/RNA Shield™ Fecal Collection Tube R1101 containing 9 ml of DNA/RNA-shield (Zymo Research, Irvine, CA, USA), according to the manufacturer’s instructions. The sample was mixed…

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MELT-SINGLE “priors” list usage

I’m trying to get “priors” working with MELT-SINGLE but nothing I’ve done seems to be making a difference. As a test, I run 1 sample without a priors list  java -Xmx6G -jar MELT/MELTv2.2.2.jar Single -bamfile HT-7604-01A-11D-2088.bam -t MELT/me_refs/Hg38/ALU_MELT.zip -h hg38.chrXYM_alts.fa -n MELT/add_bed_files/Hg38/Hg38.genes.bed -w HT-7604-01A-11D-2088-run1/ Command Line:MELT.jar Single -bamfile HT-7604-01A-11D-2088.bam -t…

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HDAC3 deacetylates H3K27ac and H3K9ac on the TrkC promoter to exacerbate sevoflurane-induced neurotoxicity

Apai C, Shah R, Tran K, Pandya Shah S (2021) Anesthesia and the developing brain: a review of sevoflurane-induced neurotoxicity in pediatric populations. Clin Ther 43:762–778 Article  CAS  PubMed  Google Scholar  Chai G et al (2022) Sevoflurane inhibits histone acetylation and contributes to cognitive dysfunction by enhancing the expression of…

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NGS Updates from ASHG: What’s New in Sequencing?

As expected, the NGS companies were sharing their news, out in full force, at the annual American Society for Human Genetics (ASHG) meeting last week in Washington, DC. Whether the updates came from the expo booths showcasing instruments, or users sharing data in the lecture halls, each company had progress…

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ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications | BMC Bioinformatics

Pipeline architecture and configuration file Genomic data processing poses a challenge for genetic research studies because it involves multiple program dependency installations, vast numbers of samples with raw data from various next-generation sequencing (NGS) platforms, and inconsistent genetic variant ID and/or positions among datasets. The Iliad suite of genomic data…

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10 AI Code Generation Trends: See Examples

Artificial Intelligence (AI) has become an integral part of various disciplines, and software development is no exception. With the advent of AI, code generation has witnessed significant advancements.  Today, AI applications can independently generate code, simplifying and accelerating the software development process. Exploring AI and code generation Introducing AI-generated coding…

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Characteristics of Klebsiella pneumoniae co-infections

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tuberculosis), is a prominent issue in the field of global public health, particularly in lower-middle-income-countries. Nearly two-thirds of global TB cases come from eight countries, including China.There are 780,000 new TB cases in China every year.1 TB is characterized by increased risk…

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Alignment prior to passing SAM/BAM to DEXSeq

Alignment prior to passing SAM/BAM to DEXSeq 1 For passing BAM/SAM files to DEXSeq. I understand that this program will take input bam/sam files that were generated using a genome aligner (eg STAR, etc). Question: are there specific recommendations/guidance for the associated run mode on a given aligner, especially for…

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UniProt: A0A8U0V2F9_MUSPF

ID A0A8U0V2F9_MUSPF Unreviewed; 413 AA. AC A0A8U0V2F9; DT 12-OCT-2022, integrated into UniProtKB/TrEMBL. DT 12-OCT-2022, sequence version 1. DT 03-MAY-2023, entry version 4. DE SubName: Full=Protein C-ets-1 isoform X5 {ECO:0000313|RefSeq:XP_044936298.1}; GN Name=ETS1 {ECO:0000313|RefSeq:XP_044936298.1}; OS Mustela putorius furo (European domestic ferret) (Mustela furo). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC…

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OpenAI Leaks GPT Builder Ahead of DevDay 2023

OpenAI’s first-ever developer conference DevDay is scheduled for today at 11:30 pm IST. Chief Sam Altman shares the developer community’s enthusiasm as they eagerly await the event.  However, a recent report unveiled a series of important conference updates that got leaked.  Firstly, Gizmo V8, the latest prototype of ChatGPT, boasts…

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bash – Racon: empty overlap set!

Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then converted from bam to fastq using samtools, then trimmed using nanofilt from there…

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South Sudan: IPC Acute Food Insecurity and Malnutrition Snapshot l September 2023 – July 2024 – South Sudan

Attachments Overview The acute food insecurity in South Sudan remains worrying with the latest data showing that 5.83 million people (46.3 percentage of the population) are experiencing high levels of acute food insecurity classified as IPC Phase 3 or above (Crisis or worse). An estimated 35,000 people are in IPC…

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zero counts for all genes in RNAseq data of Ferret

zero counts for all genes in RNAseq data of Ferret 0 I have bulk RNAseq data from Ferret and trying to get counts per gene. to do so I used hisat2 and got the genome from here: hgdownload.soe.ucsc.edu/goldenPath/musFur1/bigZips/musFur1.2bit after aligning the fastq files I used htseq and the following command:…

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