from strandex import FastqSampler sampler = FastqSampler('read1.fastq', fastq2='read2.fastq', nreads=100000, seed=42) for read1, read2 in sampler: # read1 and read2 are 4-line strings sampled from paired input sampler = FastqSampler('read1.fastq', nreads=100000, seed=42) for read...
The sampled lagoons presented low nutrient concentrations typical of oligotrophic waters, but contained levels of chlorophyll a , a proxy for phytoplankton biomass, characteristic of meso‐ to eutrophic waters. Two 18S rDNA hypervariable sites, the V4 and V8–V9 regions, were amplified from the ...
In binning, the genome is divided into bins of certain size, usually fixed, and reads aligned to each bin are counted. In segmentation, the genome is partitioned into a series of segments whose copy number is different from that of the adjacent segment. Therefore, although a site is not ...
between 0.7 and 1.7, and below 0.7, respectively. Figure4shows the heatmaps of the segmentation results by CODEX and CODEX2. Each row corresponds to a sample, with the first 16 samples towards the bottom
SIFA applies only to WGS data because it assumes a Poisson distribution when modeling the total number of reads at a locus. BiTSC2 generalizes the SIFA model for single-cell data by accounting for the overlap of CNAs and SNVs, modeling allelic dropouts, missing data, and sequencing errors ...
Somatic copy number alterations (CNAs) are major mutations that contribute to the development and progression of various cancers. Despite a few computational methods proposed to detect CNAs from single-cell transcriptomic data, the technical sparsity of
we counted the number of informative reads (e.g., reads that intersect with phased heterozygous SNPs) on each haplotype. We then calculated the absolute log2 ratio of the number of reads on each haplotype and integrated this ratio into the filtering models (Fig.1C). The application of our...
The average number of reads in a region of a genome is dependent on the total number of reads sampled, the length of the genome and the length of the region. We use this relationship to compute a minimum sliding window size to achieve a desired minimum confidence level of the observations...
Our notion of height will be associated to the steps of the path. We call hi(σσ) the height of the path at step i, that is, the height of the midpoint of the i-th step of the path, that in terms of the binary vector reads [Math Processing Error]hi(σσ)=σ1+σ2+⋯+σ...
AMD Secure RNG library provides a suite of APIs which developers can easily make use of in their applications. SECURE RNG PERFORMANCE Each invocation of RDRAND and RDSEED instruction reads a value from Cryptographic Co-processor block. The read operation, being an Memory-mapped I/O(MMIO)[4] ...