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ATAQ_SEQ
Introduction
1.
ATAQ basics
2.
Processing pipeline
2.1.
Pre-alignment
2.2.
Alignment
2.3.
Post alignment
2.3.1.
Filter & Dedup
2.3.2.
Prepare peak-calling
2.3.3.
Formats compare
2.4.
Peak Calling
2.5.
Post peak calling
3.
libQC (ataqc)
3.1.
TSS Enrichment
3.2.
Signal-to-Noise ratios
4.
setQC
4.1.
Modules
4.1.1.
Sample info
5.
Single-cell ATAC seq
5.1.
Process pipeline
6.
ATAQ FAQs
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ATAQ_SEQ
Lib QCs
Some concerpts:
insert size
fragment distribution
Yeild table
The aligned fraction is from bowtie2 log file, which added all mapped cases (paired mapped >=1 times, or single mapped >=1 times)
Reference
ENCODE Standards