RNA-Seq library mapping and coverage statistics
A High-Throughput Method for Illumina RNA-Seq Library Preparation.
... method, coverage biases should be relatively constant for each gene across ...different library prepara- tion ...in RNA-Seq and Levin and coworkers recently provided a detailed comparison of ...
11
Highly sensitive and ultrafast read mapping for RNA-seq analysis
... Due to the HPC implementation, we have devised a simple but powerful strategy in which the original high sensitivity of the algo- rithms is maintained without sacri ficing performance. HPG Aligner can map reads containing ...
8
MapSplice: Accurate Mapping of RNA-Seq Reads for Splice Junction Discovery
... junction coverage (the number of tags aligned to a ...3, coverage (solid red curve) is the least reliable metric and yields the worst performance in terms of junction ...
16
Platinum-seq: High-throughput mapping of small-molecule platinum adducts on cellular RNA
... expression of Saccharomyces cerevisiae treated with cisplatin and a second novel platinum(II) compound (azaplatin), using data acquired from the work in Chapter 2. Chapter 4 describes recent efforts to implement ...
159
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
... MMSEQ GS estimates. As we shall show, the regulariza- tion afforded by the Bayesian algorithm produces esti- mates with a lower error than the MMSEQ EM estimates. Moreover, it can readily be shown that for transcript ...
15
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
... X it | t ~ Pois bs M ( i it t ), (4) t ∼ Gam ( , ). (5) Again, the only lengths needed are the l t . The conju- gacy of the Poisson-Gamma model makes the sampling fast and straightforward as the full ...
16
Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers
... the library, mixing the library with a high diversity sample (spike-in), lowering sequencing cluster density, or any com- bination of the above [ 21 ...generated RNA-seq libraries from mouse ...
15
RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction
... recognizes RNA secondary structure and digests the middle of double stranded RNA ...of RNA-seq found that RNaseIII caused pile- up mapping of RNA-seq data because of its ...
16
RNA-seq assembly - are we there yet?
... diversity mapping accuracy will decrease. Therefore mapping errors may lead to incorrectly detected ...during mapping (increasing accuracy) at the cost of not mapping some unigenes at all ...
12
RNA-seq data analysis pipeline
... typical RNA-seq data analysis pipeline because it is well-documented, often updated and improved and has a wide selection of ...without mapping to the ...of library. There are three different ...
29
CRAC: An integrated approach to analyse RNA-seq reads Additional File 3 Results on simulated RNA-seq data.
... simulated RNA-seq data ...on mapping results of the size of the dataset in terms of number of reads, and hence of ...all mapping tools (Figure 3 in the ...
6
Synthetic spike-in standards for RNA-seq experiments
... external RNA standards are a pow- erful tool for routine assessment of RNA-seq experiments and during experimental and computational protocol ...distributions, library complexity, average ...
10
GC-Content Normalization for RNA-Seq Data
... of RNA-Seq data generated using the Illumina Genome Analyzer ...reads mapping to a particular gene reflects the abundance of the transcript in the sample of ...same library) for a given gene, ...
49
Studying bacterial transcriptomes using RNA-seq
... for mapping short read data [ 36–39 ], which often have the advantages of con- sidering base quality and read pair information when performing ...of mapping analyses have commonly been visualized as a graph ...
6
Normalization of RNA-Seq
... EDASeq implements four within-lane normalization methods, namely: loess robust local regression of read counts (log) on a gene feature such as GC-content ( loess ), global-scaling betwee[r] ...
11
A context-based approach to identify the most likely mapping for RNA-seq experiments
... the mapping with the fewest mismatches is usually chosen which may lead to wrong assignments due to sequencing ...reads mapping to the same expressed ...the mapping accuracy of both initial mappings ...
11
SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data
... Discussion SCRABBLE addresses several deficiencies of existing methods. First, several methods impute dropout events by using cell-cell distance, as quantified by either Euclidean distance or kernel distance. Such ...
12
RNA-seq analysis in R
... Rank the genes by statisical significance - you will need to create a new ranking value using -log10({p value}) * sign({Fold Change}).. Run fgsea using the new ranked genes and the H pat[r] ...
14
Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA seq
... single-cell RNA-seq protocol, and use standard laser capture microdissection to sample a tissue in a grid at high spatial resolution, while still covering the entire ...
12
Haplotype and isoform specific expression estimation using multi mapping RNA seq reads
... The first step in RNA-seq experiments is the prepara- tion of cDNA libraries, whereby RNA is isolated, frag- mented and synthesized to cDNA. Sequencing of one or both ends of the fragments then takes ...
15