Sample overview

Sample ID: Sample_1119
Biosample name: HT1080
Biosample type: Cell Line
Tissue type: Connective tissue
Cancer type: Fibroscarcoma
Region number: 49836
Length: 23235.522 kb
GEO/SRA ID: SRR2999317
Mean insert size: 209.232
Standard deviation: 139.243
TSS enrichment score: 15.03060
FRiP: 0.24228
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


TF footprint of HT1080


Peak annotation visualization of HT1080

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