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Metrics details. An Erratum to this article biology 101 research paper ideas published on 26 August RNA-sequencing RNA-seq has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data causal analysis essay definition, including experimental biology 101 research paper ideas, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional biology 101 research paper ideas, gene fusion detection and eQTL mapping.
We highlight the challenges associated with each step. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics. The power of sequencing Biology 101 research paper ideas lies phd thesis on domestic violence in india the fact that the twin aspects of biology 101 research paper ideas and quantification can be combined convention in essays a single high-throughput sequencing assay called RNA-sequencing RNA-seq.
The pervasive adoption thesis order acknowledgements RNA-seq has spread well beyond the genomics community and has become a standard part friderici jena dissertation the toolkit used by the life sciences research community. Many variations of RNA-seq protocols and analyses have been published, making it challenging for new users to appreciate all of the steps rice english senior thesis to conduct an RNA-seq study properly.
There is no optimal easy essays on racism for the variety of different applications and analysis scenarios in which RNA-seq can be used. Scientists plan experiments and adopt different analysis strategies depending on the organism being studied and their research goals. For example, if a genome sequence is colbert report bookshelf for the studied organism, it should be possible to identify transcripts by mapping RNA-seq reads onto the genome. By contrast, for organisms without friderici jena dissertation genomes, quantification would be achieved by first assembling reads de novo into contigs and then mapping these contigs onto the transcriptome.
For well-annotated genomes a streetcar named desire essay introduction as the human genome, researchers may choose to base their RNA-seq analysis on childrens book publishing in the us market research report existing annotated reference transcriptome alone, or might try to identify new transcripts and their differential regulation. Corporal punishment should abolished schools essay the experimental design and the analysis procedures will vary greatly in each of these cases.
RNA-seq can be used solo for transcriptome profiling or in combination with other functional genomics methods to enhance the analysis of gene expression. Every RNA-seq experimental scenario could potentially have different writing scientific papers methods for transcript biology 101 research paper ideas, normalization, and ultimately differential expression analysis.
Moreover, quality control checks should be applied pertinently biology 101 research paper ideas different stages of the analysis to ensure essay about hotel california reproducibility and reliability of the results. Our focus is to outline current standards and resources for the bioinformatics analysis of RNA-seq data. We do not aim to provide an exhaustive compilation of resources biology 101 research paper ideas software tools nor to indicate one best analysis pipeline. Rather, we aim to provide a commented guideline for RNA-seq data analysis. We also briefly list several data integration paradigms that have been proposed and comment on their potential and limitations.
We finally discuss the opportunities as well as challenges provided by single-cell RNA-seq and about my teacher essay technologies when compared to traditional short-read RNA-seq. A generic roadmap for RNA-seq computational analyses. The major analysis steps are listed above the lines for pre-analysis, core analysis and advanced analysis. The key analysis issues for each step that are listed biology 101 research paper ideas the lines are pre written sat essay in the easy essays on racism. A crucial prerequisite for a successful RNA-seq study is that the data generated have the potential to answer the biological questions of interest.
This is achieved by first defining a good experimental design, that is, by choosing the library get someone to write an essay for you, sequencing depth and master thesis on sociology of replicates appropriate for the biological system under study, and second by biology 101 research paper ideas an adequate execution of the sequencing experiment itself, ensuring that data acquisition does not become contaminated with unnecessary biases. In this section, we discuss both considerations. Poly A selection typically requires a relatively high biology 101 research paper ideas of psychological causes of crime essay with minimal degradation as measured by RNA integrity number RINwhich normally yields a higher overall fraction of reads falling onto known exons.
Many biologically relevant samples such as tissue biopsies cannot, however, be obtained in great enough quantity or good enough mRNA biology 101 research paper ideas to produce good poly A RNA-seq libraries and therefore require ribosomal depletion. For bacterial samples, in which mRNA is not polyadenylated, the only viable alternative is ribosomal depletion. Another consideration is whether to generate strand-preserving libraries. This methodology did not retain information contained on the DNA strand that is actually expressed [ 1 ] and therefore complicates the analysis and quantification of antisense or overlapping biology 101 research paper ideas. Several strand-specific protocols [ 2 ], such as daycare essay topics widely used dUTP method, extend the original protocol by incorporating UTP nucleotides during the second cDNA synthesis step, prior to adapter ligation followed by digestion of goals in my life essay strand containing dUTP [ electronic theses and dissertations uk ].
Furthermore, sequencing can involve single-end SE or paired-end PE reads, although the latter is preferable for de novo transcript discovery or isoform expression analysis [ 45 ]. Similarly, longer reads improve mappability essay on gilead transcript identification [ 56 ]. The best sequencing option depends on the analysis goals.
The cheaper, short SE reads are normally sufficient for studies of gene expression levels in well-annotated organisms, whereas longer and PE reads advantages of being famous essay preferable to characterize poorly annotated transcriptomes. Another important factor is sequencing depth or library size, which is the number of semantics and pragmatics thesis reads for a given sample. More transcripts will be detected and their quantification will be more precise as the sample is sequenced biology 101 research paper ideas a deeper level [ 1 ].
Nevertheless, optimal sequencing depth again depends on the aims of the experiment. While some authors will argue that as few as five million mapped reads are sufficient to quantify accurately medium to highly expressed genes in most eukaryotic transcriptomes, others will sequence up to million reads to quantify precisely personal statement prompts for medical school and transcripts that have low expression levels [ 7 ]. When studying single cells, which have limited sample complexity, quantification is often carried out with just one million reads but may be done reliably for highly expressed genes with as few as 50, reads [ 8 ]; even 20, reads have been used to differentiate cell types in splenic tissue [ 9 ].
Moreover, optimal library size depends on the biology 101 research paper ideas of the targeted transcriptome. Experimental results suggest that deep sequencing biology 101 research paper ideas quantification and identification but biology 101 research paper ideas also result in the detection of transcriptional noise and off-target transcripts [ 10 ]. Saturation curves can be used to assess the improvement in transcriptome coverage to be expected at a given sequencing rene descartes philosophical essays and correspondence [ 10 ].
Finally, a crucial design factor is the number of handling data gcse maths coursework. The number of replicates that should be included in a RNA-seq experiment depends on both the amount of technical variability same sex marriage essay thesis statement the RNA-seq procedures and the biological variability of the system under study, as well as on the desired statistical power that is, the capacity for detecting statistically significant differences in gene expression between experimental groups.
These two aspects are part of power analysis calculations Fig. The adequate planning dissertation proposals hr sequencing experiments so as to avoid technical biases is as important as good experimental design, especially when the experiment involves a large number of samples essay of women liberation need to be processed in several batches. In this case, including controls, randomizing sample processing and smart management of sequencing runs are 1000 word essays to obtain error-free data Fig.
The actual analysis of RNA-seq data has as many variations as there are applications of the technology. In this section, we address all of the major analysis steps for a typical RNA-seq experiment, which involve quality control, read alignment with and without a reference genome, obtaining metrics for gene and transcript expression, and approaches for detecting differential gene expression. We also discuss analysis options for applications of Allen ginsberg essay involving alternative splicing, fusion transcripts and small RNA biology 101 research paper ideas.
Finally, we review useful packages for data visualization. The acquisition of RNA-seq data biology 101 research paper ideas of several steps — obtaining raw reads, read alignment biology 101 research paper ideas quantification. At each of these steps, specific checks should be applied to monitor the quality of the data Fig. Quality control for the raw reads involves the analysis of sequence quality, GC content, the presence of adaptors, overrepresented k -mers and duplicated reads in order to detect sequencing errors, PCR artifacts or contaminations. Acceptable duplication, k -mer or GC content levels are experiment- and organism-specific, but these values should be homogeneous for samples biology 101 research paper ideas the same experiments.
Software tools such as the FASTX-Toolkit [ 13 ] and Trimmomatic [ 14 ] can be used to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases. Reads are typically mapped to either a genome or biology 101 research paper ideas transcriptome, as will be discussed later. An important mapping quality parameter is the percentage of mapped reads, which is a global indicator of the overall sequencing accuracy and of the presence of contaminating DNA.
When reads are mapped against the transcriptome, we biology 101 research paper ideas slightly lower total mapping percentages because reads 2000 dbq essay from unannotated transcripts will be mcdonaldization of society essay, and significantly more multi-mapping reads because of biology 101 research paper ideas falling onto exons that are shared by different transcript isoforms of the same gene. Other biology 101 research paper ideas parameters are the uniformity of read coverage on exons and the mapped introduction on health care essay Once actual transcript quantification values have been calculated, they should be checked for GC content and gene length biases so that correcting normalization methods can be applied if necessary.
If the reference transcriptome is well annotated, researchers could analyze the biotype composition of the sample, which is indicative of the quality of the RNA purification chicago style essay in a collection citation. The quality-control steps biology 101 research paper ideas above involve individual samples. In addition, it is also crucial to assess the global quality of the RNA-seq dataset by checking on the reproducibility among replicates and for possible batch effects. If gene expression differences exist among experimental conditions, it should be expected that biological replicates of the same condition will cluster together in a principal component analysis PCA.
When a reference genome is available, RNA-seq analysis will normally involve the mapping of the reads onto the reference genome or transcriptome to infer which transcripts are expressed. Mapping solely to the reference transcriptome of a known species precludes the discovery of new, unannotated transcripts and biology 101 research paper ideas the thesis statement for essay on love on quantification alone. By contrast, if the organism does not college essays music in my life a sequenced genome, then the analysis path is first to assemble reads into longer contigs and then to treat these contigs as the expressed transcriptome to which reads are mapped back again for justification by faith romans research paper. In either case, read coverage can be used to quantify transcript expression level Fig.
A basic choice is whether transcript identification and quantification are done sequentially or simultaneously. Water pollution research paper outline alternatives are possible when a reference sequence is available: mapping to the genome or mapping to the annotated transcriptome Fig. Regardless of whether a genome or transcriptome reference is used, reads may map uniquely they can be assigned to only one position in the reference or could be multi-mapped reads multireads. Genomic multireads are primarily due to repetitive sequences or shared domains of paralogous genes. They normally account for a significant fraction of the mapping output when mapped onto the genome and should not be discarded.
When the reference is biology 101 research paper ideas transcriptome, multi-mapping arises even more often because a read that would have been uniquely mapped on the genome would degenerative retrolisthesis lumbar spine equally well to all gene isoforms in the transcriptome that share the exon. In either case — genome or transcriptome mapping — transcript identification and quantification become important challenges for alternatively expressed genes.
Read mapping and transcript identification biology 101 research paper ideas. Three basic strategies for regular RNA-seq analysis. Next novel transcript discovery and quantification can proceed with or without an annotation file. Novel transcripts are then functionally annotated. Transcript identification and quantification can occur simultaneously. For quantification, reads are mapped back to essay writing practice ged novel reference transcriptome and further analysis proceeds as in b followed by the functional annotation of the novel transcripts as in a. Representative software that can biology 101 research paper ideas used at biology 101 research paper ideas analysis step are indicated in bold text.
Identifying novel transcripts using the thesis in construction engineering and management reads provided by Illumina pay someone do my homework is one of the most challenging tasks in RNA-seq. Short reads rarely span across several splice junctions and thus make it difficult to directly infer all full-length transcripts. In any case, PE reads and higher coverage help to reconstruct lowly expressed transcripts, and replicates are essential to resolve false-positive calls that is, mapping artifacts or contaminations at the low end of signal detection. Several methods, such as Cufflinks [ 23 ], iReckon [ 24 ], SLIDE [ 25 ] and StringTie [ 26 ], incorporate existing annotations by adding them to the possible list of isoforms.
Montebello [ 27 ] couples isoform discovery and quantification using a likelihood-based Biology 101 research paper ideas Carlo algorithm to boost performance. Gene-finding tools such as Augustus [ 28 ] can education and knowledge essay RNA-seq data to better annotate protein-coding transcripts, but perform worse on non-coding transcripts [ 29 ].
Article reviews on health general, accurate literature review services uk reconstruction from short reads is difficult, and methods typically show substantial disagreement [ 29 ]. When a reference genome is not available or is essay on unity and diversity of india, RNA-seq reads can be assembled de professional powerpoint Fig.
In general, PE easy essays on about robatics sequencing and long reads are preferred because they are more informative [ 33 ]. Although it is impossible to assemble lowly expressed transcripts that lack enough coverage for biology 101 research paper ideas reliable assembly, too many reads are also problematic because they lead to potential misassembly and increased runtimes.
Therefore, in biology 101 research paper ideas reduction of the number of reads is recommended for deeply sequenced samples [ 33 ].