Sample overview

Sample ID: Sample_1199
Biosample name: HCASMC
Biosample type: Other
Tissue type: Other
Cancer type: Hemoglobinopathies
Region number: 9874
Length: 4323.368 kb
GEO/SRA ID: GSM1939569
Mean insert size: 203.863
Standard deviation: 164.530
TSS enrichment score: 8.05431
FRiP: 0.05816
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


TF footprint of HCASMC


Peak annotation visualization of HCASMC

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