Quality assessment is the first step in data analysis, it provides a statistical metrics and visual information about the raw data. The results can be used to identify samples which should be excluded from the analysis, and also provides information about parameters of downstream analysis.
RNA-Seq or Whole Transcriptome Shotgun Sequencing can be used to get qualitative and quantitative information about gene expression and regulation. A complete application consisting of several RNA-Seq specific tools provides you the visualization of expression profiles, listing of differently expressed genes and alternative splice variants.
Copy Number Variation (CNV)
The application enables genome-wide identification of copy number variations. After mapping the reads from the studied and the control samples, CNV tools analyze read distributions comparatively by utilizing complex statistical methods. Genomic locations where read densities are significantly different are detected and indicated as CNV.
Multiple Sequence Alignment
Multiple Sequence Alignment is developed for arranging different sequences to find similarities and differences between them. The sequences can be extremely long (like a whole genome), differing in length, and containing insertions, deletions, and variants relative to another sequence. The MSA application enables the alignment of all the sequences in a given query set to ensure the identification of conserved sequence regions or the establishment of evolutionary relationships by constructing phylogenetic trees.
The concept for the miRNA-Seq is basically the same as for the conventional RNA-Seq: align the reads and establish quantitative profile from the alignment. The difference is made by the specific algorithms that are suited for the process and alignment of the extremely short miRNAs. The alignment of those short sequences requires extraordinary accuracy and confidence for a reliable result.
Further processing the result of the read alignment, genomic alterations are identified, these include single nucleotide polymorphisms (SNP) or single nucleotide variant (SNV) calls and InDel calls.