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Sequencing depth

Tìm thấy 17+ kết quả cho từ khóa "Sequencing depth"

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

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In particular, reducing the number of RNA samples (sce- nario A1), reducing both the number of RNA samples and sequencing depth (scenario A2), reducing the sequenc- ing depth (scenarios A3 and A4), pooling of RNA samples (scenarios B1 and C1), pooling and reducing the number of RNA samples (scenarios B2 and C2), pooling and reduc- ing the sequencing depth (scenarios B3 and C3), and both (i.e. pooling, reducing the sequencing depth and reduc- ing the number of RNA samples, scenarios B4 and C4)..

An integrated software for virus community sequencing data analysis

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Several frequently used programs for both global and local multiple sequence alignments are included in the tool MultipleSeqAlign, including Clustal W version 2.0 [18], MUSCLE [19] and Clustal Omega [20].. ð p i ln p i Þ= lnN [21], where p i represents the frequency of each type of strain in the quasispecies population, and N corresponds to the sequencing depth.

A transcriptional landscape of 28 porcine tissues obtained by super deepSAGE sequencing

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Super deepSAGE obtained ~ 5 million reads per sample with an average sequencing depth of 71X (total number. A total of 32,213 transcripts were cov- ered by Super deepSAGE. Saturation was seen very early in Super deepSAGE sequencing data due to low tag complexity (number of tags) in libraries (Fig.

Transcriptomic and presence/absence variation in the barley genome assessed from multi-tissue mRNA sequencing and their power to predict phenotypic traits

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Even with a sequencing depth that corresponds to 0.5% of that of our study, prediction accu- racies higher than that of the prediction with the SNParray data set were obtained. However, the variability of the prediction accuracy across the different runs of the resam- pling simulations increases with a reduced sequencing depth..

Using short read sequencing to characterise balanced reciprocal translocations in pigs

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To test the impact of sequencing coverage on the ability to discover the RT, we reduced the sequencing depth of the carriers to 10, 15, and 20 fold coverage and reran the pipeline to detect the RTs. For each case, the sequencing depth was reduced by random selection of 30, 50, and 60% of the trimmed reads. IGV images of the aligned reads at the breakends on both chromosomes involved in the reciprocal translocation of each detected RT in 6 of the 7 carriers.

Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion

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Higher number of genes detected in EMBR-seq is not dependent on the sequencing depth. coli op- erons in EMBR-seq. Gene transcript count correlation between different input total RNA amounts in EMBR-seq. Single-cell sequencing of the small-RNA transcriptome

Characterizing the properties of bisulfite sequencing data: Maximizing power and sensitivity to identify between-group differences in DNA methylation

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In contrast the gain in power with increased read depth is much less pronounced when detecting a mean DNAm difference of 0.10, and there is very little power at any read depth to detect a DNAm difference of 0.05. increased sample size, as read depth filtering alone will not be sufficient. The relationship be- tween read depth and power was previously also found in WGBS data, with higher total sequencing depth in- creasing the true positives detected [38]..

Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units

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Similarly, se- quencing depth and sample richness were highly corre- lated in the ASV method, leading to an underestimation of the community richness at lower sequencing depths in diverse bacterial communities (Fig.

Efficient COI barcoding using high throughput single-end 400 bp sequencing

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It is also worth noting that two blank samples retrieved COI barcodes using the default parameter settings – minimum read num- ber requirement of 10 - reaching a read support number of 13.5 and 12.5, respectively. parameter setting for the minimum read number sup- port should be adjusted case by case according to the sequencing depth and the read number of the blank samples..

Comparison of multiple algorithms to reliably detect structural variants in pears

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DENOM and Platypus, the number of SVs increased as sequencing depth increased to 50×. For Pindel, BreakDancer, DELLY, Lumpy, Sniffles and SVIM, the number of SVs called ob- viously increased as the sequencing depth increased.. 2 Comparison of the number of genes within SVs identified using NGS-based software and long-read sequencing-based software.

High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction siteassociated DNA sequencing

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In this study, the average sequencing depths of ‘Cabernet sauvignon’ and ‘Zuoyouhong’ were 24.01 and 19.40, re- spectively, the sequencing depth distribution of the hy- brid offspring is shown in Additional file 2: Fig. A total of 11,643 SNP markers were anchored into 19 linkage groups of the paternal parent with a total genetic length of 1791.21 cM. For the male map, nearly half of the linkage groups contained the regions of Gap >.

Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

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We randomly selected CKA sheep (n = 10) for the study from 305 individuals scattered on the prairie [26].. spectrophotometry (IMPLEN, CA, USA), and the Qubit®. 15 Avgqual:20 Minlen:35 Tophred:33) was used to trim the sequencing reads, and FASTQC was used to assess the quality of the raw sequencing data. The average sequencing depth was obtained for the 10 CKA sheep was 7.68×.

Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica

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The sequencing depth of the parental lines was about 2.69-fold in Yugu18 and 3.43-fold in Jigu19 and covered 18.35 and 20.36 % of the whole genome, re- spectively. After removing of the genetic variations with no differ- ences between two parents and the genetic loci which were heterozygous or absent in any parent, 74,698 SNPs and 5,737 indels were considered as effective variants (Table S2)..

PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome

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The ~ 20% Illumina short reads which were not aligned to the reference full-length transcriptome may result from the sequencing depth of the PacBio RSII platform.. Collectively, we have generated 60,353 high-quality non- redundant full-length transcripts, 3588 AS events, 40,347 complete CDS and 1273 lncRNAs of C. This study provides, for the first time, a full-length transcriptome of C.

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

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Finally, cytosine-level methy- lation calls are (optionally) obtained with METHimpute, a Hidden Markov Model for inferring the methylation status/level of individual cytosines, even in the presence of low sequencing depth and/or missing data. The aim of the interface is to improve useability and to reduce human error arising from typing mistakes or from the misspecification of parameter settings during pipeline configuration.

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing

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For each of GC content, sequencing depth, repeat content, gene count, and DpnII restriction sites, the significance of the differences between long and short arms was assessed with Welch’s two-sided T test as well as a nonparametric Mann-Whitney test imple- mented in R (Suppl. The results of the two tests were largely in agreement, but groups were only in- dicated as significantly different if they both produced significance values below 0.05 ( p <.

Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton

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The average sequencing depth of the parent lines and the offspring pools was 30.92×. The B maintainer line sequencing depth was 16.03×, whereas the sequen- cing depth of the filial BC 1 F 1 generation was 47.77. More specifically, this locus was located in the region of 25.61 Mb–59.94 Mb (34.33 Mb) using the SNP-index and G’ value method.. Fine mapping of the Rf 2 gene. We found 6 recombinant plants in the BC 1 F 1 population.

Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms

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The increased depth that can be achieved with short reads is thus more important to the completeness of the final genome assembly than the in- creased resolution provided by long-read sequencing.. As long-read sequencing technology improves, it may eventually be possible to sequence complete chromo- somes of most organisms in a single contiguous read..

Metagenomic diagnosis of severe psittacosis using multiple sequencing platforms

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Illumina generated an average depth of 1.50× and 1.21× for the sputum and blood sample, while MinION had an average depth of 1.00× for the BALF sample.. Divergent results on the BGISEQ-500 platform. Coverages of the C. The depth of the C.

PaCBAM: Fast and scalable processing of whole exome and targeted sequencing data

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To deal with the computa- tionally intensive task of calculating depth of coverage and pileup statistics at specific chromosomal regions and/or positions, different tools have been developed. Most of them, including specific modules of SAMtools [1] and BEDTools [2] and the most recent Mosdepth [3], only measure and optimize the computation of depth of sequencing coverage. provide instead statistics at single-base resolution, which.