Sample overview

Sample ID: Sample_0951
Biosample name: GM02171
Biosample type: Cell Line
Tissue type: Fibroblast
Cancer type: Normal
Region number: 65219
Length: 16472.26 kb
GEO/SRA ID: SRR5878907
Mean insert size: 67.469
Standard deviation: 42.099
TSS enrichment score: 17.96010
FRiP: 0.12697
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of GM02171

Use these accessible chromatin regions to analyze or download

TF footprint of GM02171


Peak annotation visualization of GM02171

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