Maverix Analytic Platform analysis overview for exosome RNA-seq
Sequencing data is analyzed for quality and contamination. Raw reads are trimmed to remove adapters, then trimmed and filtered based on quality scores. The scores used for trimming and filtering are specific to the sequencing platform. The preprocessed reads are then assessed for quality and plots are generated of per base quality before and after trimming.
Sequence reads are mapped to the genome and mapping statistics are generated. BAM files with chromosomal location of mapped reads and the alignment quality are made available for visualization in the integrated UCSC Genome Browser.
Abundance levels for ncRNAs (miRNAs, tRNAs, rRNAs, lincRNAs, piRNAs, snoRNAs), antisense transcripts, coding genes and repeat elements (LTR, LINE, SINE, and tandem repeats) are determined. A summary of reads overlapping each of these annotations is created and provided in the form of pie-charts.
Differences in expression of ncRNA, antisense transcripts, and repeat elements between samples are calculated. Visual representation of the analysis results are provided, including interactive tabular and heat map views linked to the integrated genome browser.