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104 results for “BAM”
IMPROVER: the new probabilistic post processing system at the UK Met Office: BAMS paper Data
<p>© Crown Copyright, Met Office</p> <p>This is the data associated with the figures in the IMPROVER BAMS paper 2023: <a href="https://doi.org/10.1175/BAMS-D-21-0273.1">https://doi.org/10.1175/BAMS-D-21-0273.1</a>.</p> <p>Gridded data is in CF-NetCDF with reasonably self explanatory metadata, other data such as for Figure 9's wind speed calibration is in CSV.</p>
BAM reference data: results of ASTM E139 -11 creep tests on a reference material of Nimonic 75 nickel-base alloy
<p>Results of creep tests on a certified reference material at T = 600°C and a tensile creep load of 160 MPa are provided. The raw data are available in ASCII format (*.lis files). <br> The file "Inhalt_Content_V1.1.pdf" contains further information about the files provided.<br> The evaluated results include the times to reach 2% and 4% creep strain, respectively, and the creep rate after 400 h.</p> <p>The tests were carried out in an accredited test laboratory. The calibrations of all measurands and test and measuring equipment are documented. The calibrations meet the requirements of the test procedure and are metrologically traceable.</p>
Heteroplasmy Benchmark Dataset - mitochondrial DNA mixture model - MiSeq - U5-H1-M1-M2-M3-M4-M5 - BAM
<p>mtDNA mixture model of 2 mtDNA sequences belonging to haplogroups U5 and H1. Run on Illumina MiSeq with 3 different polymerases (Clontech, Herculase, NEB Taq), and different DNA extraction protocols - <strong>BAM FILES </strong></p> <p>M1 = Mixture 1:2 i.e. 50%</p> <p>M2 = Mixture 1:10 i.e. 10%</p> <p>M3 = Mixture 1:50 i.e. 2%</p> <p>M4 = Mixture 1:100 i.e. 1%</p> <p>M5 = Mixture 1:200 i.e. 0.5%</p>
Simulated Ancient Genomic Kinship Dataset: BAM (5x run7-12) Files for Related (including inbred) Pairs
<p>Simulated Ancient Genomic Kinship Dataset: VCF and BAM (5x (run7-12) Files for Related (including inbred) Pairs</p> <p><strong>Description:</strong></p> <p>This dataset comprises simulated pedigrees (VCF files containing 8,677,101 autosomal biallelic and 298,625 X chromosomal SNP positions) generated using Ped-sim (v1.3) and comprising pairs of diverse familial relationship types up to third-degree. The first-degree relationships are parent-offspring and siblings; the second-degree relationships are half-siblings, grandparent-grandchild, and avuncular pairs; and third-degree relationships are first cousins, great-grandparent-great-grandchild, and grand avuncular pairs. For each of these 8 relationship types, our dataset includes 48 pairs of individuals. It also contains unrelated pairs. Additionally, the dataset includes first- and second-degree relatives, with inbreeding (parent-offspring pairs where the parents of the offspring are the first cousins and grandparent-grandchild pairs where the grandchild is the offspring of first cousins). Our simulations encompass all combinations of kinship types regarding sex. The dataset was further enriched by simulating ancient DNA-like sequencing data (5x and 1x BAM files) of Ped-sim simulated individuals using the gargammel tool, employing procedures akin to standard paleogenomic sequencing libraries. Note that the BAM files contain only randomly chosen 200K autosomal SNP positions. Positions can be found in the "200K_positions" file. Details can be found in Aktürk, Mapelli and Güler et al. 2023.</p> <p><strong>Data Sources and Generation:</strong></p> <p>Founder genotypes for pedigree simulation were created from the Tuscany (TSI) population SNPs within the 1000 Genomes Dataset v3. Notably, the founder genotypes lack background relatedness or runs of homozygosity (ROH).</p> <p><strong>Description of File Naming Conventions:</strong></p> <p>The naming conventions of the BAM files in this dataset are designed to convey key information regarding the specifics of each file.</p> <p><strong>cov1x or cov5x:</strong> This segment denotes the coverage level of the BAM files, indicating whether the sequencing coverage for the individuals in the files is 1x or 5x.</p> <p><strong>run_*:</strong> Signifies the particular batch from which the pedigree and individuals are derived. This name segment also applies to VCF files.</p> <p><strong>parent-offspring_* or similar identifiers:</strong> Reflects the origin of the individual from the corresponding VCF file. For instance, "parent-offspring_1" corresponds to the individuals present in the "run_*_parent-offspring_1.vcf" file.</p> <p><strong>parent-offspring* or similar identifiers: </strong>Indicates the origin of the individual from the sets within the VCF files. For example, "parent-offspring1" signifies the first set of parent-offspring pedigrees within the VCF file. Note that parent-offspring, grandparent-grandchild, and great-grandparent-great-grandchild and the inbreeding VCFs contain only one set, so this identifier is always 1. This convention can be 1 or 2 for the rest of the pedigrees, as the VCF files contain two sets of related pairs.</p> <p><strong>_g*-b*-: </strong>Provides information about the individual's generational level within the VCF. This follows the Ped-sim syntax. For example, for parent-offspring type, "_g1-b1-" indicates the first parent (generation 1) within a specific pedigree, and "_g1-b2-" indicates the second parent (generation 1) while "_g2-b1-" represents the offspring (generation 2).</p> <p><strong>Example Naming Structure:</strong></p> <p>For instance, the file "cov1x_run1_parent-offspring_1_parent-offspring1_g1-b1-i1.all.hs37d5.cons.90perc.trimBAM.bam" signifies a BAM file with 1x coverage, originating from "run1," containing individuals from the "run_*_parent-offspring_1.vcf" file (first set of parent-offspring pairs) where "_g1-b1-" designates the first parent in the first generation. The latter half of the name "hs37d5.cons.90perc.trimBAM.bam" is the same across all files. </p> <p><strong>Note1:</strong> Segments such as <strong>parent-offspring*_g*-b*- </strong>can also be tracked in the naming of the genotype columns in the VCF.</p> <p><strong>Note2: </strong>Sexual information within the VCF files is discernible from the genetic data present at X chromosome positions. Individuals carrying two genotypes on the X chromosome are female, while those with a single genotype are male.</p> <p><strong>Note3: Some of the individuals from distinct pedigrees may</strong>,<strong> in fact</strong>,<strong> be related due to shared ancestry through common founders. To suit specific research objectives, researchers may need to identify and exclude such relatives if the full dataset is used for kinship estimation.</strong></p> <p>For more details about the dataset's generation process, unique characteristics, or any specific inquiries, our team is available for further information. We welcome and encourage inquiries, aiming to provide comprehensive support and additional details that might aid researchers in utilizing this dataset effectively. Please don't hesitate to contact us for any specific information you may need.</p> <p>This repository contains only cov5x BAM files (run7-12). The rest of the files can be found at <strong>10.5281/zenodo.10079685 </strong>and<strong> 10.5281/zenodo.10070958.</strong></p> <p> </p>
Experimental raw data sets associated with certified reference material BAM-P116 (titanium dioxide) for comparison of nitrogen and argon sorption, available in the universal adsorption information format (AIF)
<p>These data sets serve as models for calculating the specific surface area (BET method) using gas sorption in accordance with ISO 9277.<br>The present measurements were carried out with nitrogen at 77 Kelvin and argon at 87 Kelvin.<br>It is recommended to use the following requirements for the molecular cross-sectional area:<br>Nitrogen: 0.1620 nm²<br>Argon: 0.1420 nm²</p> <p>Expected specific surface area for nitrogen (BET): 305 to 345 m²/g<br>Expected specific surface area for argon (BET): 300 to 310 m²/g</p> <p>Titanium dioxides certified with nitrogen sorption and additionally measured with argon for research purposes were used as sample material.<br>The resulting data sets are intended to serve as comparative data for own measurements and show the differences in sorption behaviour and evaluations between nitrogen and argon.<br>These data are stored in the universal AIF format (adsorption information format), which allows flexible use of the data.</p>
.bam alignment files of Illumina and ONT sequencing of pREF plasmid
<p>The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed <em>pREF</em>, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The <em>pREF</em> sequence encodes 21 synthetic genes that can be <em>in vitro</em> transcribed into spike-in mRNA controls, and <em>in vitro</em> translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of <em>pREF</em> in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, <em>pREF</em> can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides the first universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.</p>
Dataset for a tutorial to quantify BAM earthquake using SNAP
<p><strong>A tutorial to quantify BAM earthquake using SNAP</strong></p> <p>Differential InSAR is a satellite-based remote sensing technique that can be used to quantify small displacements of the Earth's surface. This is due to the interferometric phase being much more sensitive to the ground motion than to the elevation difference. This practical session will explain how to apply it to real-world Envisat ASAR images, with user-oriented open-source SNAP software. The main goal is able to generate ground motion from a pair of SAR images to map the Earthquake of 2003 in BAM city.</p> <p>More information can be found here: </p> <p>Video: https://youtu.be/Uc-5F9Vz04w</p> <p>https://github.com/BAMInSAR</p> <p>https://www.facebook.com/groups/RadarInterferometry</p>
Hepatitis B Virus - Geneious BAM files
<p>BAM files for specimens assembled in Geneious including their genotype specific references.</p>
Pieve di Santa Cristina - test BAMS
Pieve medievale di Santa Cristina, Montichiari, Brescia, Italy. Test con sole immagini da drone di Stefano Rodella - BAMS. Verifica pesi e caratteristiche tecniche. Retopo a 200k. Source: Objaverse 1.0 / Sketchfab
BAM files of wild-type CP-A cells and the TP53 KO CP-A clones.
<p>BAM files (alignment to hg38) of wild-type CP-A cells and the TP53 knock-out (KO) CP-A clones (2c8, 3d2, 5f4). Please refer to Figure 2. of <span>doi:</span> https://doi.org/10.1101/2024.01.24.576991.</p>
Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [FACS + BAMs + tables]
<div>FACS data related to Figures 1 and 4 in Schwämmle et al. 2025. </div> <div>Also include BAM files of published data and other files needed to replicate analyses included in https://github.com/EddaSchulz/TFiScreen_Paper. </div>
Junction bam files for Drosophila species
<p>Junction bam files for Drosophila species</p>
Heteroplasmy Benchmark Dataset - mitochondrial DNA mixture model - HiSeq - M1-M4 - BAM
<p>Illumina HiSeq data of mixtures M1 (50%), M2 (10%), M3 (2%) and M4 (1%) of haplotypes H1c6 and U5a2e (decreasing).</p> <p>See <a href="https://doi.org/10.1371/journal.pone.0135643">https://doi.org/10.1371/journal.pone.0135643</a> for technical/lab-related informations</p>
Experimental raw data sets associated with certified reference material BAM-P115 (titanium dioxide) for comparison of nitrogen and argon sorption, available in the universal adsorption information format (AIF)
<p>These data sets serve as models for calculating the specific surface area (BET method) using gas sorption in accordance with ISO 9277.<br>The present measurements were carried out with nitrogen at 77 Kelvin and argon at 87 Kelvin.<br>It is recommended to use the following requirements for the molecular cross-sectional area:<br>Nitrogen: 0.1620 nm²<br>Argon: 0.1420 nm²</p> <p>Expected specific surface area for nitrogen (BET): 140 to 154 m²/g<br>Expected specific surface area for argon (BET): 129 to 135 m²/g</p> <p>Titanium dioxides certified with nitrogen sorption and additionally measured with argon for research purposes were used as sample material.<br>The resulting data sets are intended to serve as comparative data for own measurements and show the differences in sorption behaviour and evaluations between nitrogen and argon.<br>These data are stored in the universal AIF format (adsorption information format), which allows flexible use of the data.</p>
Experimental raw data sets associated with certified reference material BAM-P114 (titanium dioxide) for comparison of nitrogen and argon sorption, available in the universal adsorption information format (AIF)
<p>These data sets serve as models for calculating the specific surface area (BET method) using gas sorption in accordance with ISO 9277.<br>The present measurements were carried out with nitrogen at 77 Kelvin and argon at 87 Kelvin.<br>It is recommended to use the following requirements for the molecular cross-sectional area:<br>Nitrogen: 0.1620 nm²<br>Argon: 0.1420 nm²</p> <p>Expected specific surface area for nitrogen (BET): 24 to 25 m²/g<br>Expected specific surface area for argon (BET): 20 m²/g</p> <p>Titanium dioxides certified with nitrogen sorption and additionally measured with argon for research purposes were used as sample material.<br>The resulting data sets are intended to serve as comparative data for own measurements and show the differences in sorption behaviour and evaluations between nitrogen and argon.<br>These data are stored in the universal AIF format (adsorption information format), which allows flexible use of the data.</p>
Example BAM file
<p>This BAM file is intended for use in software examples, when users don't have access to other data.</p> <p>Snyder et. al (2016) made the the original BAM file publically available. It was downloaded from https://kircherlab.bihealth.org/download/cfDNA/</p> <p>The following steps were performed:</p> <ol> <li>We filtered the reads to only keep fragments with insert sizes in [100bp, 220bp].</li> <li>We downsampled to keep only 10% of the fragments. The file is likely only useful for seeing the software run.</li> <li>We remapped the file to hg38.</li> </ol> <p>[1] Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell. 2016 Jan 14;164(1-2):57-68. doi: 10.1016/j.cell.2015.11.050. PubMed PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/26771485" rel="nofollow">26771485</a></p> <p> </p>
nPSize BAM images as 2D arrays
<p>BAM1.zip BAM2.zip BAM3.zip are 2D arrays, to be extracted in the following directory: /dataset/images/BAM to build /dataset/images/BAM/[BAM_images.h5] Note: h5 is a compressed format, to uncompress.</p>
Calibration of BAM using the SLICS simulation
<p>The calibration of the BAM kernel and bias using the SLIC simulation as a reference reaches percent accuracy in the halo power spectrum.</p>
CRM BAM-A001 eCerto data file
<p>Data file (RData) containing measurement data recorded during the production process of the Certified Reference Material <strong>BAM-A001 </strong> containing Polycyclic Aromatic Hydrocarbons (PAH) in Olive Oil. The data can be most conveniently opened using the Shiny-App eCerto which is accessible at <a href="https://www.bam.de/eCerto">https://www.bam.de/eCerto</a>.</p>
Brain and Meditation (BAM) Study
ClinicalTrials.gov study NCT05215314. IPD Sharing: YES. Countries: 1. Publications: 1.
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