diffenent to reference DNA sequencing RNA-seq ChIP-seq ATAC-seq
bulk single-cell transcriptome
Why is RNA-seq read mapping hard? errors in the reads (mismatches, insertions, deletions) errors in the reference genetic variation spliced mapping reads contains sequences in 2exons multi-mapping efficiency columns are samples rows are genes
each condition multiple samples make assumption about the structure of the data dot is a gene low variance - artifacts reduce false positive maximize statistical power
overlap between two set of genes in random genes
some reads just map to one genome some reads map to two genomes but better
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UMI unique molecular identifier 10x company offers single cell sequencing
significant difference pvalue for
cell cycle effect a lot genes change expression in cell cycle
order cell along pseudotime based on expression
mRNA transcribed and degradated go to different state