Using Curio for Expression Analysis
Curio's approach for analyzing NGS sequence data (as part of either an RNA-seq or DNA-seq experiment) to calculate and
analyze the expression of different genomic features (transcripts, genes, etc.) can be summarized to include the following functionality:
Ability to quantify the expression of transcripts (or corresponding genes) from unaligned read data (i.e. raw FASTQ files)
by automatically assembling an index of the nucleotide sequence for each defined transcript from its individual exons
and then matching each read to the best transcript sequence.
Ability to quantify the expression of genomic features of aligned read data by analyzing how the reads overlap
with individual generic features (i.e. exons or arbitrary genome ranges) or meta features (i.e. transcripts or genes)
by analyzing the mapping positions of each aligned read in relation to a standard or custom set of genomic features.
Visualize, compare, or download various expression metrics (TPM, RPKM, expressed read count, transcript length, etc.) across
Calculate and visualize the differential expression of multiple groups of samples.
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