Data Analysis

Compression of High Throughput Sequencing Data

Data volumes generated by next-generation sequencing (NGS) technologies is now a major concern for both data storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as the widely used gzip method. Researchers ...

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SATRAP – SOLiD Assembler TRAnslation Program

rna-seq

SOLiD DNA sequences are typically analyzed using a reference genome, while they are not recommended for de novo assembly of genomes or transcriptomes. This is mainly due to the difficulty in translating the SOLiD color-space data into normal base-space sequences. ...

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List of RNA-Seq bioinformatics tools

rna-seq

from: https://en.wiki2.org/wiki/List_of_RNA-Seq_bioinformatics_tools 1 Quality control and pre-processing data 1.1 Quality control and filtering data 1.2 Detection of chimeric reads 1.3 Errors Correction 1.4 Pre-processing data 2 Alignment Tools 2.1 Short (Unspliced) aligners 2.2 Spliced aligners 2.2.1 Aligners based on known splice junctions (annotation-guided aligners) 2.2.2 De novo Splice Aligners 2.2.2.1 De novo Splice Aligners that also use annotation optionally 2.2.2.2 Other Spliced Aligners 3 Normalization, Quantitative analysis and Differential Expression 3.1 Multi-tool solutions 4 Workbench (analysis pipeline / integrated solutions) 4.1 Commercial Solutions 4.2 Open (free) Source Solutions 5 Alternative Splicing Analysis 5.1 General Tools 5.2 Intron Retention Analysis 6 Bias Correction 7 Fusion genes/chimeras/translocation finders/structural variations 8 Copy Number Variation identification 9 RNA-Seq simulators 10 Transcriptome assemblers 10.1 Genome-Guided assemblers 10.2 Genome-Independent (de novo) assemblers 10.2.1 Assembly evaluation tools 11 Co-expression networks 12 miRNA prediction 13 Visualization tools 14 Functional, Network & Pathway Analysis Tools 15 Further annotation tools for RNA-Seq data 16 RNA-Seq Databases 17 Webinars and Presentations ...

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RNA-Seq Analysis Pipeline Based on Oshell Environment

rna-seq

Advances in transcriptome sequencing (RNA-Seq) have revolutionized the way to characterize and quantify transcripts. The breakthroughs in RNA-Seq technologies give rise to the ever-increasing volumes of data, making data processing the bottleneck of transcriptome research. It becomes crucial to develop ...

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Normalization of RNA-Seq Data Exercises

rna-seq

from RPubs – by Prasanth A S In order to explain the different methods of normalization and their problems with large array of data, which are assumed to have: most genes are not differentially expressed across conditions. the distribution of ...

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