Sample overview

Sample ID: Sample_0036
Biosample name: nucleus accumbens
Biosample type: Tissue
Tissue type: Brain
Cancer type: Normal
Region number: 55776
Length: 33823.528 kb
GEO/SRA ID: SRR5343852
Mean insert size: 199.233
Standard deviation: 149.426
TSS enrichment score: 40.78780
FRiP: 0.07870
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of nucleus accumbens

Use these accessible chromatin regions to analyze or download

TF footprint of nucleus accumbens


Peak annotation visualization of nucleus accumbens

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