mRIN - Assessing mRNA integrity directly from RNA-Seq data.HTSeq The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.Kraken: A set of tools for quality control and analysis of high-throughput sequence data.
Results are presented in HTML permanent reports. This tool provides an overview to inform about problematic areas, summary graphs and tables to rapid assessment of data. Import of data is possible from FastQ files, BAM or SAM format. FastQC is a quality control tool for high-throughput sequence data ( Babraham Institute) and is developed in Java.dupRadar An R package which provides functions for plotting and analyzing the duplication rates dependent on the expression levels.bam-lorenz-coverage A tool that can generate Lorenz plots and Coverage plots, or export these statistics to text files, directly from BAM file(s).AfterQC - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.Often, is necessary to filter data, removing low quality sequences or bases (trimming), adapters, contaminations, overrepresented sequences or correcting errors to assure a coherent final result. Quality assessment of raw data is the first step of the bioinformatics pipeline of RNA-Seq. Quality control, trimming, error correction and pre-processing of data ssizeRNA Sample Size Calculation for RNA-Seq Experimental Design.Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.
PROPER: PROspective Power Evaluation for RNAseq.Some important questions like sequencing depth/coverage or how many biological or technical replicates must be carefully considered. Here are listed some of the principal tools commonly employed and links to some important web resources.ĭesign is a fundamental step of a particular RNA-Seq experiment. This technique is largely dependent on bioinformatics tools developed to support the different steps of the process. RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies.
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