Sample overview

Sample ID: Sample_1301
Biosample name: Mixture of GM12878 and HEK293T
Biosample type: Cell Line
Tissue type: Blood
Cancer type: Normal
Region number: 11007
Length: 4887.734 kb
GEO/SRA ID: SRR1947692
Mean insert size: 232.943
Standard deviation: 178.730
TSS enrichment score: 5.30141
FRiP: 0.14827
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of Mixture of GM12878 and HEK293T

Use these accessible chromatin regions to analyze or download

TF footprint of Mixture of GM12878 and HEK293T


Peak annotation visualization of Mixture of GM12878 and HEK293T

Plot A

Plot B

Plot A: a pie chart of annotated genomic features.
Note A: the proportion of annotating genomic region (Promoter, 5'UTR, 3'UTR, Exon, Intron, Downstream and Intergenic).
Plot B: a heatmap of peaks binding to TSS region.
Note B: the profile of ATAC peaks binding to TSS region (+/- 1kb).

Software and parameters used

Read mapping: bowtie2(v2.2.5) -p 10 -X 2000 -x -S
Duplicates Removing: picard MarkDuplicates REMOVE_DUPLICATES=true ASSUME_SORTED=true
Peak calling: macs2(2.1.2) --broad--SPMR --nomodel --extsize 200 -q 0.01
Trimming the adapter: trim_galore --phred33 --stringency 3 --length 20