Report for Biomek_20th_2018-06-26

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Sample info.

	Sample Index (from MSTS)	sample ID (from MSTS)	Label (for QC report)	species	Sequencing ID	Experiment type	Machine
JYH_501	SAMP-159	GM19240	GM19240_3.	Human	JYH_501	ATAC-seq	NextSeq550 Mid
JYH_502	SAMP-159	GM19240	GM19240_2.	Human	JYH_502	ATAC-seq	NextSeq550 Mid
JYH_503	SAMP-159	GM19240	GM19240_1.75.	Human	JYH_503	ATAC-seq	NextSeq550 Mid
JYH_504	SAMP-159	GM19240	GM19240_1.5.	Human	JYH_504	ATAC-seq	NextSeq550 Mid
JYH_505	SAMP-159	GM19240	GM19240_1.25.	Human	JYH_505	ATAC-seq	NextSeq550 Mid
JYH_506	SAMP-159	GM19240	GM19240_1.	Human	JYH_506	ATAC-seq	NextSeq550 Mid
JYH_507	SAMP-159	GM19240	GM19240_0.75.	Human	JYH_507	ATAC-seq	NextSeq550 Mid
JYH_508	SAMP-159	GM19240	GM19240_0.5.	Human	JYH_508	ATAC-seq	NextSeq550 Mid
JYH_509	Other	HepG2	HepG2_3.	Human	JYH_509	ATAC-seq	NextSeq550 Mid
JYH_510	Other	HepG2	HepG2_2.	Human	JYH_510	ATAC-seq	NextSeq550 Mid
JYH_511	Other	HepG2	HepG2_1.75.	Human	JYH_511	ATAC-seq	NextSeq550 Mid
JYH_512	Other	HepG2	HepG2_1.5.	Human	JYH_512	ATAC-seq	NextSeq550 Mid
JYH_513	Other	HepG2	HepG2_1.25.	Human	JYH_513	ATAC-seq	NextSeq550 Mid
JYH_514	Other	HepG2	HepG2_1.	Human	JYH_514	ATAC-seq	NextSeq550 Mid
JYH_515	Other	HepG2	HepG2_0.75.	Human	JYH_515	ATAC-seq	NextSeq550 Mid
JYH_516	Other	HepG2	HepG2_0.5.	Human	JYH_516	ATAC-seq	NextSeq550 Mid

Fastq files

Sequence sources (potential contamination)

Sequencing Quality

Per base N Content

Mean Quality Scores

Per Sequence Quality Scores

Per Sequence GC content

Sequence Duplication Levels

Sequence Length Distribution

see details (leave setQC)

Mappability

Reads yeild table

Read yield (%) after each step

Read counts after each step

Mitochondrial reads fraction

TSS enrichment

TSS enrichement plots

GM19240_3. : 48.38

GM19240_2. : 44.19

GM19240_1.75. : 45.23

GM19240_1.5. : 45.04

GM19240_1.25. : 45.04

GM19240_1. : 43.32

GM19240_0.75. : 43.65

GM19240_0.5. : 48.89

HepG2_3. : 24.84

HepG2_2. : 23.69

HepG2_1.75. : 23.97

HepG2_1.5. : 24.74

HepG2_1.25. : 23.53

HepG2_1. : 23.51

HepG2_0.75. : 22.36

HepG2_0.5. : 23.63

Average TSS enrichement compare

Max TSS enrichement compare

FROT (Fraction of reads overlap TSS)

Insert size & GC bias

Insert size distribution

GC bias in final bam

Peaks

Peak basics

Raw peak numbers

FRiP (Fraction of reads in Peak region)

Peak advanced

Correlation matrix & Peak Intensity Scatter

PCA

LibQC table

Tracks & Download

Browser

Open WashU Genome Browser in a new window

Batch download

click 'Download file list' link bellow to download a 'files.txt' that contains the list of urls to files in this report. Then run the script bellow on the terminal

Download file list

xargs -n 1 curl -0 -L < files.txt

Download links