Sample overview

Sample ID: Sample_0644
Biosample name: EpiSC line from P. Tesar
Biosample type: Stem Cell
Tissue type: Embryo
Cancer type: Normal
Region number: 2961
Length: 814.001 kb
GEO/SRA ID: SRR5815120
Mean insert size: 86.790
Standard deviation: 62.181
TSS enrichment score: 6.71040
FRiP: 0.17904
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of EpiSC line from P. Tesar

Use these accessible chromatin regions to analyze or download

TF footprint of EpiSC line from P. Tesar


Peak annotation visualization of EpiSC line from P. Tesar

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