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Welcome to the Seq2C wiki!

Seq2C is a program for copy number analysis from targeted DNA-seq with or without control normal. It works for both PCR-based ultra-deep sequencing on limited number of genes and exome or even WGS. It requires a BED file annotated with genes and aligned BAM file to run. Seq2C is gene-centric, and produce results at gene level by default. It also performs breakpoint analysis within genes, such as exon level deletions/amplification in BRCA1/2, PTEN, etc.

When running without control normal, Seq2C relies on cohort statistics for normalization. So please the sample size is relative large (> 10, ideally > 30) and the cohort are heterogenous, e.g. no amp. or deletion of a gene exceeds 50% of samples. When running samples shared the same origin (e.g. resistant clones), please ensure to include a normal diploid as control, or there'll be systemic shift of amplified or deleted genes.

AUTHOR

Zhongwu Lai ([email protected])