Sample overview

Sample ID: Sample_0690
Biosample name: HFF
Biosample type: Cell Line
Tissue type: Foreskin
Cancer type: Normal
Region number: 76449
Length: 42811.214 kb
GEO/SRA ID: GSM2688940
Mean insert size: 190.554
Standard deviation: 140.987
TSS enrichment score: 35.62540
FRiP: 0.20449
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


TF footprint of HFF


Peak annotation visualization of HFF

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