Sample overview

Sample ID: Sample_0550
Biosample name: MCF7
Biosample type: Cell Line
Tissue type: Mammary Gland
Cancer type: Breast cancer
Region number: 40244
Length: 14812.73 kb
GEO/SRA ID: SRR6372046
Mean insert size: --
Standard deviation: --
TSS enrichment score: 11.18100
FRiP: 0.15949
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.

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TF footprint of MCF7


Peak annotation visualization of MCF7

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