Tag: BWA

Senior Bioinformatics Software Developer – Bethesda

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

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Samtools flagstat confusing result of a merged bam file

Hi, I am a bioinformatics student and I am struggling with an issue, I had paired-end fastq files for one sample with some low-quality bases at the end and adapter contamination, so I went and I trimmed my reads with trimmomatic, it gave me 4 files that I used for…

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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

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samtools sort

samtools sort 1 I am transforming sam files to bam, to facilitate their ordering I use this command, % cd /Volumes/GENOMA/BWA % samtools sort -n -O V350019555_L03_B5GHUMqcnrRAABA-551.sam | samtools fixmate -m -O bam V350019555_L03_B5GHUMqcnrRAABA-551.bam but it gives me the following error, As elsewhere in samtools, use ‘-‘ as the filename…

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Bwa on multiple processor

Hi Guys, When I am trying to run bwa mem on multiple processor, I am getting error as : > mpirun -np 16 bwa mem hg19-agilent.fasta R1.fastq R2.fastq | samtools sort -o aln.bam [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read…

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Alignment report

Alignment report 0 Hi Guys, I did alignment of R1 and R2 fastq files with reference genome using bwa mem and got bam file. Now, I want to check whether the alignment is done correctly and alignment percentage,coverage etc. I run following command: bwa mem hg19.fasta R1.fastq R2.fastq | samtools…

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sequence alignment – MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds

[*] I have been trying to follow the GATK Best Practice Workflow for ‘Data pre-processing for variant discovery’ (gatk.broadinstitute.org/hc/en-us/articles/360035535912). This has all been run on Windows Subsystem for Linux 2 on the Bash shell. I started off with FASTQ files from IGSR (www.internationalgenome.org/data-portal) and performed alignment with Bowtie2 (instead of…

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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Significance Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids…

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Benchmarking the NVIDIA Clara Parabricks germline pipeline on AWS

This blog post was contributed by Ankit Sethia, PhD, and Timothy Harkins, PhD, at NVIDIA Parabricks, and Olivia Choudhury, PhD,  Sujaya Srinivasan, and Aniket Deshpande at AWS. This blog provides an overview of NVIDIA’s Clara Parabricks along with a guide on how to use Parabricks within the AWS Marketplace. It…

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Towards the biogeography of prokaryotic genes

1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed  Google Scholar  2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS  PubMed  PubMed Central  Google Scholar  3. Mohammad,…

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Attempting to generate a bam.bai file but the output is not readable

Attempting to generate a bam.bai file but the output is not readable 1 Hi, I am new a exome sequencing, and have tried to follow tutorials on the subject. I am stuck at the samtools index stage because the output files are in a non-human readable format and I believe…

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Padding out a GVCF file with 1000G exomes to get gatk VariantRecalibrator working with a small sample

I’ve got sequencing data for a small 500 bp amplicon from a few samples. GATK best principles suggest running VariantRecalibrator on the GVCF files I generate. I’m trying to get this working, but I get an error about “Found annotations with zero variances”. Reading the gatk manual and other posts…

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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

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Why are my Nextflow processes not executing in parallel?

I have written a Nextflow script with three process: The first process takes a pair of fastq files and aligns with reference genome. The process writes the resulting SAM file into sam channel. Second process takes input from the sam channel and creates a BAM file from it, and writes…

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Weird error from BWA and BOWTIE2

Weird error from BWA and BOWTIE2 1 Hi community, Recently I have used BWA and Bowtie2 to align simulated DNA sequencing data to test our sequencing simulator. I got some errors from both aligners: BWA: submit.sh: line 48: 6881 Segmentation fault (core dumped) BOWTIE2: terminate called after throwing an instance…

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Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

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iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

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Dissemination of Mycobacterium abscessus via global transmission networks

Dataset construction, cluster identification and definition of DCCs Whole genome sequencing of two collections of isolates from Manchester, UK, and the Netherlands was carried out as previously described2. Briefly, DNA was extracted from colony sweeps of subcultured samples before to paired-end sequencing using the Illumina HiSeq platform. These samples were…

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Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 CAS  PubMed  PubMed Central  Article  Google Scholar  Alexander DH, Shringarpure SS, Novembre J, Lange K (2015) Admixture 1.3 software manual. UCLA Hum Genet Softw Distrib, Los Angeles Google Scholar  Angert AL, Bontrager…

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converting Bam to fastq while removing clipping(hard/soft clip bases)

converting Bam to fastq while removing clipping(hard/soft clip bases) 0 Hello, I want to do some analysis and my raw data is paired-end reads fastq files. So far: I used BWA mem to convert them to Sam file then used samtools to convert to BAM file. My next step is…

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Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova

Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…

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The sardine run in southeastern Africa is a mass migration into an ecological trap

INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…

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Align fastq SOLiD data

Align fastq SOLiD data 1 Hello everyone, I have downloaded some data from the short read archive using the sratoolkit. The data is SOLiD data. I have seen people using the Lifescope (Life Technologies) to align the reads, as I presume it works for this type of data. But unfortunately,…

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bamdst gives error “EOF marker is absent. The input is probably truncated.”

bamdst gives error “EOF marker is absent. The input is probably truncated.” 0 I created a set of bam files from Poolseq data using bwa -aln, and all of the output files gave the following error when I ran bamdst to get summary statistics on read depth: “EOF marker is…

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High tumor mutation burden and DNA repair gene mutations

Introduction Anaplastic lymphoma kinase (ALK)‑fusion genes represent a small but important part of oncogenic driver mutations in NSCLC, accounting for approximately 3%‑7% of all cases worldwide.1,2 Small molecule tyrosine kinase inhibitors (TKIs) are the standard therapy for ALK-rearranged NSCLC. Crizotinib, a first-generation TKI, is the most widely used targeted drug…

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Command-line alternative to Geneious assemble for Sanger sequencing data

I am doing Sanger sequencing of a construct ~2Kb using 4 primer pairs. I get back 4 .ab1 files, each with generally around 1Kb of high quality sequence and given the relatively small size of the construct these overlap significantly. The goal is to assemble these 4 sequences into a…

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Bioinformatics Support Specialist (Remote) at Agilent Technologies, Inc.

Agilent inspires and supports discoveries that advance the quality of life. We provide life science, diagnostic, and applied market laboratories worldwide with instruments, services, consumables, applications, and expertise. Agilent enables customers to gain the answers and insights they seek so they can do what they do best: improve the world…

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High frequency of an otherwise rare phenotype in a small and isolated tiger population

Significance Small and isolated populations have low genetic variation due to founding bottlenecks and genetic drift. Few empirical studies demonstrate visible phenotypic change associated with drift using genetic data in endangered species. We used genomic analyses of a captive tiger pedigree to identify the genetic basis for a rare trait,…

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MAPQ (Mapping quality) of 0 for most reads from BWA-MEM2 (with no secondary alignment or other apparent reason)

Hello, I got a very weird output from BWA-mem2 – most of the reads have mapping quality of 0, even though there is no secondary alignment or anything else suspicious. I got sequencing data that was aligned with Novoalign to hg18, the data was bam files. I needed to realign…

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Biocept, Inc. hiring Bioinformatics Scientist in San Diego, California, United States

Tasks and Responsibilities Develop and maintain analysis pipelines for next generation sequencing data. Deep dive analysis of targeted and UMI… Required Skills & Experience MS/PhD in bioinformatics, mathematics, computer science, biology, chemistry, or similar, with 3+ years experience in an industrial environment. Experience in clinical diagnostics desired but not required…

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Cancer Mutation Detection Depends on Choices at Each Step of Sequencing, Analysis Pipeline

NEW YORK — An international team of researchers has examined how variations in sequencing approaches can influence the ability to accurately detect cancer mutations, providing guidance for the wider community. The team additionally developed a set of reference samples for benchmarking efforts. Next-generation sequencing approaches are increasingly being adopted to…

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Assistant Research Professor – Genomics and Bioinformatics job with City of Hope

About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope…

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ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

    Significance To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth…

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Mapping digested synthetic oligos back to original sequences.

Mapping digested synthetic oligos back to original sequences. 0 Hi, I have several synthetic dsDNA of 70bp and I digest them with some enzyme. I am interested to see the exact cut site of the enzyme so I had the products sequenced using MiSeq. They are single-end read. What is…

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Aligning Multiple paired end files together

Aligning Multiple paired end files together 1 Hi All, I have 72 paired end .fastq file for which i need to do Alignment using BWA. Since its a paired end data and my files are named as sam_001_1.fastq sam_001_2.fastq sam_002_1.fastq sam_002_2.fastq & so on Since its a paired end data…

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Gene mutation analysis in papillary thyroid carcinoma

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

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pseudogenes and their parent gene common regions

pseudogenes and their parent gene common regions 1 Hi,I have a list of gene names and their corresponding pseudogenes. I want to figure out which regions of a pseudogene and its parent gene are common. I think one way would be first extracting their sequence then align them to each…

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How to analyze the generated VCF file, what to do if you have multiple VCF file for the same gene?

How to analyze the generated VCF file, what to do if you have multiple VCF file for the same gene? 0 I have given 40 tumor samples to NGS for the analysis and I gave them a list of specific genes only do the sequencing for lets call that gene…

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Twist Bioscience hiring Bioinformatics Scientist, Production Bioinformatics in South San Francisco, California, United States

Twist is looking for a Bioinformatics Scientist to join our Production Bioinformatics Team. You will work alongside research scientists, software engineers and data scientists to further deliver on our mission to expand access to best-in-class synthetic biology and next-generation sequencing applications. You will be developing and engineering tools to better…

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Error in pipe output to samblaster from bwa-mem2

Error in pipe output to samblaster from bwa-mem2 0 Hi, I am trying to upgrade my command from bwa to bwa-mem2. This command usually works. bwa mem -M -R “@RGtID:idtSM:sampletLB:lib” human_g1k_v37.fasta sample.1.fq sample.2.fq | samblaster -M –excludeDups –addMateTags –maxSplitCount 2 –minNonOverlap 20 | samtools view -S -b – > sample.bam…

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the Genomic Rearrangement IDentification Software Suite

Tool:GRIDSS: the Genomic Rearrangement IDentification Software Suite 0 GRIDSS is typically used for detecting structural variation breakpoints from short read sequencing data but is a modular software suite containing a number of tools useful for the detection of genomic rearrangements including: A structural variant caller. The GRIDSS caller uses break-end…

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Bioinformatics Analyst II in Danville, PA for Geisinger

Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research. Performs and supervises complex data extraction, transformation, visualization, and summarization to support Research…

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How to align and visualize data with .fasta and .gff3 files in IGV?

How to align and visualize data with .fasta and .gff3 files in IGV? 1 Hi everyone, I have an issue in aligning and visualizing my data in IGV. As I read in manual of IGV, to align and visualize data, I need to to prepare .BAM/.SAM or other input format…

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Bowtie2 hg19 reference for gatk MuTect

Bowtie2 hg19 reference for gatk MuTect 3 Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 as the aligner, which reference file should I be using? The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2 and…

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Bwa sampe error 999

Bwa sampe error 999 25-08-2021 I’m getting the following error message when I try to import into 1aa.vremenagoda54.ru file (using samtools import). [samopen] SAM header I’m using bwa aln to find coordinates and bwa sampe to…

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Exctracting amino acid substitutions

Exctracting amino acid substitutions 0 Good day, I’m trying to develop a pipeline to determine mutations which are responsible for amino acid changes in genes associated with antibiotic resistance. I have roughly 300 bacrtial isolates. My approach so far has not been fruitful, in short this is what i tried:…

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Snakemake-Aligment using BWA-MEM2

Hello I have started using snakemake 6.5.2 to align fastq files with reference file. I have pasted the error below in this question. How to allocate memory in the snakefile and read the header from samfile, ‘-‘. This is the snakefile (wrapper for running alignment): rule bwa_mem2_mem: input: reads=[“/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.1.fq”, “/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.2.fq”]…

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Unable to locate package hisat2″

how to solve this error when I want to install HISAT2? “E: Unable to locate package hisat2” 1 Dear all, I need to install HISAT2 aligner in my study. My Linux version is 16.04 (Xenial Xerus). So I used the below command : sudo apt-get install -y hisat2 but I…

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How to calculate the Average Insert Size after mapping the reads to the reference genome using BWA

How to calculate the Average Insert Size after mapping the reads to the reference genome using BWA 3 Hi, Having mapped the reads to the reference genome using BWA, I am trying to calculate their Average Insert Size. Thereafter, I converted the BAM file to SAM file in order to…

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Missing read group in BAM files

Missing read group in BAM files 1 Hello everyone, I have processed PE reads through the pipeline HybPiper to align them to a reference genome with GATK. But inspecting the output BAM files with the GATK tool ValidateSamFile, I found out a very common error in the error report: WARNING::RECORD_MISSING_READ_GROUP…

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MarkduplicatesSpark How to speed-up ?

MarkduplicatesSpark How to speed-up ? 0 Hello all, I would like to know if there is any good option to speed up MarkduplicatesSpark ? I work with human genome with arround 900 millions reads (151 bp). I work on a cluster (with slurm). The command that i used is (with…

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What is the difference between GRCh37 and hs37? And hg19?

This is what I have found so far. Please correct me if I am wrong. GRCh37 w/o patches includes the primary assembly (22 autosomal, X. Y, and non-chromosomal supecontigs) and alternate scaffolds, but not a reference mitogenome. Non-chromosomal supercontigs are the unlocalized and unplaced scaffolds. The rCRS reference mitogenome in…

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Base recalibration -Java run time error and no sequence dictionary

Base recalibration -Java run time error and no sequence dictionary 0 Hello I am stuck with base recalibration step in NGS analysis. Used this command for the base calibration step: gatk BaseRecalibrator -I sample1.bam -R gch38.fa –known-sites GCF_000001405.39 -O recal_data.table I got the following warning: WARN IndexUtils – Feature file…

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Vacancy for Bioinformatics Analyst in the USA – OYA Opportunities

Apply for Vacancy for Bioinformatics Analyst at Weill Cornell Medicine in the USA. The deadline for this job is 30th September 2021. About: Weill Cornell Medicine, officially the Joan & Sanford I. Weill Medical College of Cornell University, is the biomedical research unit and medical school of Cornell University, a…

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So many variants detected.

So many variants detected. 0 Dear All, I have done variant calling in Germline data that has single sample of each individual and two genes. I did following steps, but after checking results I found too many variants. After Haplotypecaller (the step 6) I found 140900 known variants, and the…

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CROP-seq data analysis

CROP-seq data analysis 1 Hi, I am a new bie to single cell sequencing analysis. I have to analyze CROP-seq data, I am going through the following paper, www.nature.com/articles/nmeth.4177. I have to use cell ranger ( instead of DROP-seq software) as the first step to process single cell data.I wanted…

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Alignment using bwa-mem2

Alignment using bwa-mem2 0 Hello I need help in aligning the sequence with reference using bwa-mem2. I used the following code: bwa-mem2 mem -t 8 gch38.fa DE98NGSUKBD117612_1_1.fq DE98NGSUKBD117612_1_2.fq > d3_align.sam I got the following error: ERROR! Unable to open the file: gch38.fa.bwt.2bit.64 There is no gch38.fa.bwt.2bit.64 file. I have the…

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align using file.ht2

align using file.ht2 1 now i downloaded in my terminal indexed file of UCSC hg19 and when i uncompress it , i found two files genome.5.ht2 genome.8.ht2 and every time i want to align my samples at indexed file this error show up [e::bwa_idx_load_from_disk] fail to locate the index files…

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I am converting the fq.gz. files (which are the results of the mgi study) to bam files to view on igv.

I am converting the fq.gz. files (which are the results of the mgi study) to bam files to view on igv. 0 Hey everyone, before i start apologies for the inconvenience cause of my wrong or inappropriate use of terms. I take some fails of bwa mem lately. As i…

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Map Entire Directory of Paired-End Reads at Once

Map Entire Directory of Paired-End Reads at Once 0 Is there a way to map an entire directory of reads at once? Would I just have to write a script for this specific to my directory structure and data? I’m using BWA MEM to map 49 paired-end reads and have…

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Read group info

Read group info 0 Hello I need help in getting read group info for performing alignment using BWA-MEM2. I read previous post (bwa mem: Passing a variable to read group) on read-group info, where a shell script is used to get the read group info from fastq file. Can someone…

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