Sample ID: | Sample_0793 |
Biosample name: | iPSC-NA19138 |
Biosample type: | Stem Cell |
Tissue type: | iPSC |
Cancer type: | Other |
Region number: | 1109 |
Length: | 784.947 kb |
GEO/SRA ID: | SRR6412428 |
Mean insert size: | 125.670 |
Standard deviation: | 87.564 |
TSS enrichment score: | 2.13141 |
FRiP: | 0.00271 |
Diasgnostic plot | |
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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). |
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 |