Tag: BWA

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…

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]…

Reference genome, BWA and right algorithm 1 Hello I’m using BWA to create the index for aligning some rna-seq fastq. First thing I did was download hg38.fa.align.gz from UCSC Then I: gzip -d hg38.fa.align.gz sudo apt-get install bwa Here comes the problem. BWA instructions reccomend bwtsw algorithm, but when I…

Bwa-mem2 indexing not working down stream 0 I am using bwa-mem2 to create my index and to map my reads to the reference genome. This is my indexing code #!/bin/bash #SBATCH -J index #SBATCH -A gts-rro3 #SBATCH -N 1 –ntasks-per-node=24 #SBATCH –mem-per-cpu=8G #SBATCH -t 1:00:00 #SBATCH -o index.out cd $SLURM_SUBMIT_DIR…

Introduction Sepsis is one of the major diseases that poses a serious threat to human health, and its incidence and in-hospital mortality rates remain high despite the continuous updating of sepsis guidelines.1 Its main clinical manifestations are elevated body temperature, chills, and rapid heart rate, and it is most common…

Snakemake error AttributeError: ‘Resources’ object has no attribute ‘tmpdir’ 0 I have built a Snakemake pipeline which has been designed for paired-end reads. I have made a trial with single-end reads, and got this error. I am not sure it is related to the change of reads design, and to…

Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…

bwa-mem reproducibility 1 I have a set of paired end fastq files, and I run bwa-mem (v0.7.17-r1188) on the files with the same exact parameters, including the same number of threads, in two different computing clusters. I compare the BAM file produced via samtools stats. and the outputs are different…

Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar  Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….

Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article  CAS  PubMed  Google Scholar  Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article  PubMed  Google Scholar  Comai, L. The…

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,…

Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…

Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article  ADS  CAS  PubMed  Google Scholar  Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Srivastava, M….

Variant missing in WGS sample 1 Hi, I have processed a WGS sample including alignment (bwa-mem2), variant calling (GATK HaplotypeCaller) and annotation (ANNOVAR). In the annotated file, a variant fitting the phenotype was identified. However, on visualizing the bam in IGV, this variant was not there. What could be the…

Is interleaved Fastq files the same as interlaced fastq 0 There are errors in BWA-MEM2 that there manipulation Data • 271 views • link updated 2 hours ago by Joe 21k • written 1 day ago by RCMC • 0 Login before adding your answer. Read more here: Source link

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…

The affine gap design space for selecting variant representations As demonstrated in Fig. 1, the main issue with a difference-based format such as VCF is that often there are multiple reasonable sets of variant calls that can be used to represent the same final sequence relative to a reference FASTA. Since…

Cell culture The human endometrial carcinoma HEC-1-B cells were cultured in the modified Eagle’s medium (MEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a 5% (v/v) CO2 incubator. The human embryonic kidney HEK293T cells were cultured in the Dulbecco’s modified Eagle’s medium (DMEM) supplemented…

Bowtie 2 alignment 0 Hello All, My objective is to align paired reads against my reference genome (nematode) and I have used bowtie2 and bwa to accomplish this. The process is complete, but the alignment stats from bowtie2 doesn’t make any sense. Initially I used the –very-sensitive parameter, hence I…

Introduction Respiratory tract infections are common and occur frequently. Rapid and accurate microbial detection is essential for timely and appropriate treatment. Traditional microbial detection methods have some limitations such as dependence on morphology, long duration, low sensitivity, and high variability.1,2 Metagenomic next-generation sequencing (mNGS) is a new detection technology characterized…

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…

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…

Cell line and growth assays Cell lines were grown in Roswell Park Memorial Institute-1640 medium (RPMI-1640) with 1% penicillin–streptomycin (10,000 U ml−1) and 10% FBS or in Iscove’s modified Dulbecco’s medium (IMDM) with 1% penicillin–streptomycin (10,000 U ml−1), l-glutamine (200 mM) and 10% FBS in a humidified incubator with 5% CO2 maintained at 37 °C. Drugs…

Centers for Disease Control and Prevention (U.S.). Antibiotic Resistance Threats in the United States, 2019. doi.org/10.15620/cdc:82532 (2019). Centers for Disease Control and Prevention. COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022. doi.org/10.15620/CDC:117915 (2022). Fricks-Lima, J. et al. Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from…

Materials Animals All of the mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics. The mice were maintained under specific-pathogen-free conditions, with 2 to 5 mice housed in individually ventilated cages (Techniplast). The cages were equipped with bedding material, nesting material, a paper…

Hello, I am struggling to processing and analyse bam files (from bwa alignment), to extracting the chimeric read alignment. I am aligning human cell line RNA-seq data (paired end) to virus, aimed to find the viral integration sites in the genome. For that, after reading a bit here from following…

Analysis of Roche KAPA Target Enrichment kit experimental data obtained on an Illumina sequencing system is most frequently performed using a variety of publicly available, open-source analysis tools. The typical variant calling analysis workflow consists of sequencing read quality assessment, read filtering, mapping against the reference genome, duplicate removal, coverage…

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…

Mapping quality in `vg giraffe` 0 I ran vg giraffe to get the GAF file. I have some questions about the 12th column, that is mapping quality(MAPQ). The difference of MAPQ standard between aligners makes me confused. I found MAPQ is in the range[0, 60] which similar with bwa-mem, but…

Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar  Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article  CAS  PubMed  Google…

Introduction Patients with persistent, recurrent, or metastatic (P/R/M) cervical carcinoma respond poorly to treatment despite the best available therapeutic regimens, with a 5-year survival of 17%.1 Most of them are heavily pretreated with chemotherapy and/or radiotherapy, and many patients experience complications related to treatment or advanced disease, which exclude them…

BWA mem align reads with MQ = 0 to only one region (reference genome has two similar sequences). 1 So, i use WBA mem to align my reads (from NGS panels) to reference genome. My reads align to two different, but very similar regions. I want to prevent align these…

Abstract Mycobacterium avium complex (MAC) infections are a significant clinical challenge. Determining drug-susceptibility profiles and the genetic basis of drug resistance is crucial for guiding effective treatment strategies. This study aimed to determine the drug-susceptibility profiles of MAC clinical isolates and to investigate the genetic basis conferring drug resistance using…

Find all locations of aligned reads with MQ (Mapping Quality) = 0. 1 I have white reads in BAM file with MQ = 0. I know that it means that reads align to multiple locations. I know location of one align, but can i find another location/locations in IGV? If…

How to align a genome fasta file from NCBI to a reference genome? 1 Hi, I want to align a genome published on NCBI (scaffold level) to a reference genome (chromosome level). I though bwa mem could work, but it is stuck, running for too long without any error message….

Hello, We have been trying to develop a target capture sequencing of around one hundred regions in the human genome. The probes capture a region of approximately 500bp around some genetic variants of interest. Our bioinformatics pipeline uses bwa-mem for aligning the captured reads to a custom genome reference. These…

BaseRecalibrator takes forever to run. Any suggestions? 1 Hello, I am trying to run BaseRecalibrator tool from GATK package and it takes forever (more than 4 days per one bam file). The command I’m using is: gatk BaseRecalibrator -I NG-01_1_S1_dedup_bwa.bam -R /rumi/shams/genomes/hg38/hg38.fa –known-sites Mills_and_1000G_gold_standard.indels.hg38.vcf.gz –known-sites 1000G_phase1.snps.high_confidence.hg38.vcf.gz –known-sites Homo_sapiens_assembly38.dbsnp138.vcf -O NG-01_1_S1_dedup_bwa_BSQR.table…

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…

Mice The research conducted in this study complied with all of the relevant ethical regulations. The animal protocols were approved by and performed in accordance with the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. C57BL/6, OT-I50, pmel51 and Rosa26-Cas9 knock-in52 mice were purchased from The…

INTRODUCTION Microbiome research, especially the detection of microorganisms by molecular techniques, has become a fundamental tool for investigating host-associated bacteria, such as those harbored by veterinary or human clinical samples[1,2]. Next-generation sequencing (NGS) approaches now enable the identification of slow-growing, non-cultivable, or non-viable bacteria contained in clinical specimens without relying…

Early Customers Realize 10x Increase in Performance and Cloud Cost Savings; Sentieon Software Offered Free in Memory Machine Cloud Subscription MILPITAS, Calif., Nov. 14, 2023 /PRNewswire/ — MemVerge®, pioneers of Big Memory software, and Sentieon®, the market leader in genomics software, today announced a collaboration to accelerate next-generation sequencing (NGS)…

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…

BWA mem -M option for gatk mutect 0 Hi, everyone! I am new to the gatk pipelines, so I’m not sure is it necessary to use the -M option in the bwa men commond before I put the outcoming bam file to the gatk mutect pipelines for calling the mutation…

Introduction Brucellosis is a common zoonotic infection in most of the developing regions of the world, severely affecting livestock productivity and human health. It caused by a small, nonmotile gram-negative coccobacillus of the genus Brucella. Among reported human brucellosis cases, the pathogenic strain B. melitensis is the most frequently encountered.1,2…

bcftools mipileup error: format error, unexpected A at line 1 0 I had a problem using bcftools. After using the command line(below): there is some error in my results. The error message stated: “Note: none of –samples-file, –ploidy or –ploidy-file given, assuming all sites are diploid [E::fai_build_core] Format error, unexpected…

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…

1. Introduction Cervical cancer (CC) is the third most common cancer in women worldwide and has a high mortality rate among women. In 2008, CC was responsible for 275,000 deaths, thereby being the fourth leading cause of cancer death in females worldwide.[1,2] In China, CC is the second most…

I am setting up a Snakemake pipeline for sequencing reads alignment and variants calling. But the samtools index rule is not activated, and the subsequent haplotype caller rule fail. I think it is because the samtools index rule is not perceived as necessary to execute the output of rule all…

Ethic statement The Clinical Research Ethics Review Committee of Kyushu University Hospital approved the study (permit no. 29-43, 30-268, and 700-00). Written informed consent for the current research project was obtained before the tumor tissue, and a blood sample were harvested. This study was also conducted according to the principles…

In partnership with a major Life Science organization we are seeking candidates for a summer Biological Data Analysis Internship based out of Rockville, MD. This is a 10 week Summer internship for 2024. Expected start date is June 3rd through August 9th, 2024. This is a 40 hour/week; 100% remote…

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…

Hello, I’m trying to write a simple bwa script for my research, but it keeps failing. I have two questions in this post. The first code can be executed, but only the first paired fastq files are processed. Google search tells me it’s because the index_ch is a queue channel…

Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….

Can clumpify.sh be used in a streaming fashion downstream of bcl-convert 0 Hi I wanted to know if it is possible to use clumpify.sh in a streaming fashion – like one would do with bwa mem …. | samtools I would like to demultiplex with bcl-convert and on the fly,…

Human induced pluripotent stem cells (iPSCs) Reprogramming and Culture This study was ethically approved by the Medical Ethics Committee of Nanjing Maternal and Child Health Care Hospital (2021KY-131), and informed consents were obtained from the patient’s legal guardian as well as the healthy donors, in accordance with the Declaration of…

1. Install bwa-mem2-git via UAR with a Helper – YAY a. Install YAY (github.com/Jguer/yay) pacman -S –needed git base-devel git clone aur.archlinux.org/yay.git cd yay makepkg -si b. Install bwa-mem2-git on Arch using YAY yay -S bwa-mem2-git c. Remove bwa-mem2-git on Arch using YAY yay -Rns bwa-mem2-git 2. Install bwa-mem2-git via…

Introduction The non-random packaging of chromatin within the nucleus is a universal feature of eukaryotic genomes. The three-dimensional (3D) spatial organization of chromatin could be partitioned at different levels based on the interaction frequency between two given loci in the genome. Advances in sequencing technologies have led to the identification…

Are XA: tagged reads == SA: tagged BWAMEM aligned reads? 1 I have a simple question. I am interested in reads with secondary alignments. I have a script that will parse out reads with secondary alignments for bwa-mem BAM files. These reads are tagged with SA: My problem is that…

Primary samples and nucleic acid extraction A cohort of 48 patients diagnosed with advanced adenoma (AAD), defined by size > 20 mm, or colorectal carcinoma (CRC) were collected between 2013 and 2016. The study was approved by the institutional ethics committee of Hospital General Universitario de Alicante (Ref. CEICPI2013/01), and written informed consent…

I have issues when running a wrapper of BWA mem with Snakemake. The error message “No module named ‘snakemake_wrapper_utils’” appear (see below). However, when checking if the package is installed in Python, I found the following: import snakemake_wrapper_utils print(snakemake_wrapper_utils.__version__) 0.1.0 Did anyone have this problem? Would you know why there…

Ethical statement Our research complies with all relevant ethical regulations, including the Declaration of Helsinki and has been approved by the Institutional Review Boards of University of Chicago, Duke University and the Alliance to Cure Cavernous Malformations. Cerebral cavernous malformation lesions All human CCM tissue specimens have been previously reported18,19…

run-bwamem from BWAKIT does not work 1 Hi, everyone! I am currently performing HLA typing analysis using the bwakit-0.7.17 for Linux Mint 20. The problem comes when running the “run-bwamem” file, when we obtain empty output files. We have even tried to perform it through Miniconda by typing the next:…

Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…

BAC plasmids Human (CH17-203N23, CH17-449P15 and CH17-339H2) and mouse (RP23-51O13, RP23-75P20 and RP23-204E8) BACs were purchased from BACPAC Resources Center. Yeast–bacterium shuttle vector pLM1050 was modified by L. Mitchell based on a previous study28. pWZ699 was constructed by inserting a cassette containing pPGK-ΔTK-SV40pA transcription unit and the Actb gene into…

Working with UsChallenging. Meaningful. Life-changing. Those aren’t words that are usually associated with a job. But working at Bristol Myers Squibb is anything but usual. Here, uniquely interesting work happens every day, in every department. From optimizing a production line to the latest breakthroughs in cell therapy, this is work…

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Archaeological evidence indicates the presence of technocomplexes at the interface of this transition, complicating our understanding of the period and the association of those with specific hominin groups….

Study design Experiments were performed in accordance with the New Zealand Animal Welfare Act (1999) and institutional guidelines provided by the University of Auckland Animal Ethics Committee, which reviewed and approved these experiments under application R1003. We did not use any specific randomisation process to allocate animals to a particular…

!*! GENERAL SUMMARY/ OVERVIEW STATEMENT: In Gulhan Lab, we develop statistical and machine learning methods for cancer genomics to improve patient classification and early cancer detection strategies. We aim to decipher the broad spectrum of genomic instabilities that dictate the evolution of cancer genomes, and to understand how best to…

Enyu Tong,1,* Ying Zhou,1,* Zhengwei Liu,2 Yelei Zhu,2 Mingwu Zhang,2 Kunyang Wu,2 Junhang Pan,2 Jianmin Jiang1– 3 1School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China; 2Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China; 3Key Laboratory of…

You should write and render a “Methods” Rmarkdown file that describes what each script does. Retrieve the reference genome (human, release 27) from the Gencode FTP server (getGenome.sh) Retrieve the NGS reads used in the comparison paper. These are available in the SRA under accession SRR6808334 (getReads.sh) Quality trim the…

Animal models Animal studies were approved by the Institutional Animal Care Use Committee of the Institute of Biosciences and Technology, Texas A&M University (AUP 2020-0195). Most mouse strains bear a C57BL/6 genetic background unless otherwise noted. All the animals were housed in a certified animal facility with a standard dark/light…

Introduction Antimicrobial resistance is a hidden global pandemic that shattered over 4.9 million people in 2019 alone, and the burden is highest, mainly in low-resource settings.1 Drug-resistant tuberculosis (DR-TB) caused by Mycobacterium tuberculosis (Mtb) complex (MTBC), which is resistant to one or more anti-TB drugs, is a leading global public…

Rapaka, R. R. et al. Conserved natural IgM antibodies mediate innate and adaptive immunity against the opportunistic fungus Pneumocystis murina. J. Exp. Med. 207, 2907–2919 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  Boehm, T., Iwanami, N. & Hess, I. Evolution of the immune system in the lower vertebrates. Annu….

Hey everybody, I have just performed the alignment of paired-end reads to a reference using bwa mem with the -M flag, ran samtools markdup and flagstat. Flagstat produced the following output: 4985084 + 0 in total (QC-passed reads + QC-failed reads) 1806492 + 0 primary 3178592 + 0 secondary 0…

Mushroom collecting Sporocarps were collected from various herbaria and during three expeditions to Point Reyes National Seashore (PRNS), California in 2004, 2014 and 2015, and in 2015 from three sites in Portugal. A total of 86 sporocarps were collected: 67 Californian sporocarps (one early herbarium sample dates to 1993), 11…

Wyles, J. S., Kunkel, J. G. & Wilson, A. C. Birds, behavior, and anatomical evolution. Proc. Natl Acad. Sci. 80, 4394–4397 (1983). Article  CAS  PubMed  PubMed Central  Google Scholar  Lapiedra, O., Sol, D., Carranza, S. & Beaulieu, J. M. Behavioural changes and the adaptive diversification of pigeons and doves. Proc….

The Position Principal Bioinformatics Scientist We are seeking a highly skilled and experienced Principal Bioinformatics Scientist specializing in Next Generation Sequencing (NGS) to join our research team. As a Computational Biologist in NGS, you will lead and contribute to cutting-edge projects focused on analyzing and interpreting NGS data, playing a…

        NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…

  Programmable DNA, the software of Life, is finally here! Twist Bioscience is developing a disruptive Synthetic DNA technology that will change the world, enabling widespread health and sustainability. Synthetic biologists use our products to engineer how organisms produce cures to diseases; everyday chemicals are made using the atmosphere as…

Tutorial:NGS one-liner to call variants 0 This is a tutorial about creating a pipeline for sequence analysis in a single line. It is made for capture/amplicon short read sequencing in mind for human DNA and tested with reference exome sequencing data described here. I share the process and debuging steps…

Inspiration Computational Biology allows for the intersection of biology and computing for technological innovations and optimizations in genomics, modeling systems, biology, phylogenetics, etc. In our project, we chose to focus on studying the structure and function of sequences from a community of organisms, like on human skin, in the soil,…

Question on samtools view with –fast option 0 Hi I had a question on samtools view with –fast option. I was trying to find any relevant docs and/or blogs detailing its usage and how best to use it. I could not find any and I thought I will ask the…

Tutorial:NGS oneliner 0 This is a tutorial about creating a pipeline for sequence analysis in a single line.I share the process and debuging steps gone through while putting it together.Source is available at: github.com/barslmn/ngsoneliner/I couldn’t make a longer post, complete version of this post: omics.sbs/blog/NGSoneliner/NGSoneliner.html Pipeline # fastp –in1 “$R1″…

I wish to input the names of my samples in a table with the corresponding files of reads forward and reverse to use them in a Snakemake workflow: sample fq1 fq2 1 ../reads/110627_0240_AC0254ABXX_2_SA-PE-001.1.fq.gz ../reads/110627_0240_AC0254ABXX_2_SA-PE-001.2.fq.gz 2 ../reads/110627_0240_AC0254ABXX_2_SA-PE-002.1.fq.gz ../reads/110627_0240_AC0254ABXX_2_SA-PE-002.2.fq.gz 22 ../reads/110802_0249_AD0CM0ABXX_3_SA-PE-022.1.fq.gz ../reads/110802_0249_AD0CM0ABXX_3_SA-PE-022.2.fq.gz Unfortunately, the management of the wildcards is more complex and…

Cell culture and treatments DIvA (AsiSI-ER-U2OS)19, AID-DIvA (AID-AsiSI-ER-U2OS)23 and 53BP1-GFP DIvA20 cells were developed in U2OS (ATCC HTB-96) cells and were previously described. Authentication of the U2OS cell line was performed by the provider ATCC, which uses morphology and short tandem repeat profiling to confirm the identity of human cell…

Hi All, I have been trying to fetch the reads mapped to influenza virus genome (negative sense RNA) in an RNA seq. data from chicken infection experiment that I have recently done., using Fastq screen (www.bioinformatics.babraham.ac.uk/projects/fastq_screen/). It is a nice tool, where you can edit the configuration file (by adding…

Abstract Background: Processing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resource-intensive with computational demands and storage limitations that pose significant challenges that increase cost. The use of software tools independent of one another,…

Redirecting the output of a command related to another command 1 I want to get a .txt file showing the computer’s performance of gtime command related to another command: bwa mem. Bwa is a genome aligner tool. Below the code I’ve used: { gtime -v bwa mem -t 4 -R…

Introduction Welcome to circAtlas 3.0 (a gateway to consistently curated vertebrate circular RNAs). circAtlas 3.0 contains a compendium of 2,674 RNA-seq libraries from 33 normal tissues from human, macaque, mouse, rat, rabbit, cat, dog, pig, sheep and chicken. Main characteristics of circAtlas include: circAtlas uses the standardized nomenclature scheme proposed…

Cell lines Hsu and CT cells originally derived from Culex quinquefasciatus and Culex tarsalis, respectively, were used as experimental material (gifts from R. van Rij, Radboud University, Nijmegen, the Netherlands). These cell lines are known to harbor several MSV infections [7]. Aag2 and C6/36 cells were received from A. Kohl…

Finding exactly where reads map from SAM 1 Hello, I am trying to find exactly where my reads have mapped on a reference genome using information found in a SAM file. The files I am working with were generated using Bowtie1 and bwa. These tools were run with default parameters,…

Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…

Introduction Hypertrophic cardiomyopathy (HCM), characterized by asymmetric hypertrophy of the ventricular wall, is a condition where the heart becomes thickened without a distinct inducement.1,2 Epidemiological investigation shows that the estimated prevalence rate of HCM in the general population is 1:500.3,4 The clinical manifestations vary greatly, with no symptoms and mild…

Prospects of Whole Genome Sequencing in Animal Breeding The development of high-throughput sequencing technologies has revolutionized animal genetics and genomics. The widespread use of whole-genome sequencing (WGS) allows detection of a full range of common and rare genetic variants of different types across almost the entire genome which facilitates rare…

Plant material and growth conditions Nicotiana tabacum cultivar Petit Havana was used for all experiments. The TALEN design and the TALEN-expressing line Nt-JF1006-30 were described previously19. For plant growth under sterile conditions, surface-sterilized seeds were germinated on Murashige and Skoog (MS) medium52 consisting of premixed MS salts and modified vitamins…

Position: Bioinformatics Data Analyst Company: GenomicStar – A SaaS based Precision Medicine Platform Job Purpose: The Bioinformatics Data Analyst will play a critical role in the development, validation, and implementation of data analysis pipelines for various genetic test panels, incorporating state-of-the-art AI techniques. This role is integral to our commitment…

Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…

Hi there, this is more so of a hint/suggestion post than a real question since I could manage to find some related posts here on Biostars but appreciate a feedback on the procedure/results for the analysis. In principle, I’m trying to compare the bwa-mem_GATK pipeline working on the linear reference…

I am trying to make a Snakemake pipeline using a configuration file config.yaml. — samples: – Sample_1: reads/raw_reads_1 – Sample_2: reads/raw_reads_2 – Sample_3: reads/raw_reads_3 reference: – “path/to/reference.fasta” … Following the good practices given in the Snakemake wrapper repository, I have used wrappers commands as much as possible. snakemake-wrappers.readthedocs.io/en/stable/ However I…

Hey all, I’m trying to map my RADseq to a reference genome, and none of my paired-end reads are being paired. Forward and reverse reads are both mapping separately, but not pairing. This problem is consistent for all of my samples. Any help would be much appreciated!! I also viewed…