Sample overview

Sample ID: Sample_0750
Biosample name: LCL
Biosample type: Induced pluripotent stem cell line
Tissue type: Blood
Cancer type: Other
Region number: 42246
Length: 17639.716 kb
GEO/SRA ID: SRR6412828
Mean insert size: 150.741
Standard deviation: 105.166
TSS enrichment score: 19.81030
FRiP: 0.13379
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


TF footprint of LCL


Peak annotation visualization of LCL

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