Sample name: K562_RNA-seq_80

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name K562_RNA-seq_80
sample_desc 20% K562 PRO-seq + 80% K562 RNA-seq
treatment 70M total reads
protocol PRO
organism human
read_type SINGLE
umi_len 0
read1 /project/shefflab/data//guertin/fastq/K562_80pctRNA.fastq.gz
srr K562_80pctRNA
File_mb 5315.52
Read_type SINGLE
Genome hg38
Raw_reads 70000000
Fastq_reads 70000000
Reads_with_adapter 31815025.0
Uninformative_adapter_reads 349949.0
Pct_uninformative_adapter_reads 0.4999
Trimmed_reads 69650051
Trim_loss_rate 0.5
Peak_adapter_insertion_size 34
Degradation_ratio 0.2308
Aligned_reads_human_rDNA 2559080.0
Alignment_rate_human_rDNA 3.67
Mapped_reads 57718557
QC_filtered_reads 11466593
Aligned_reads 46251964
Alignment_rate 66.41
Total_efficiency 66.07
Read_depth 7.92
Mitochondrial_reads 3613062
Maximum_read_length 100
Genome_size 3099922541
NRF 0.6
PBC1 0.86
PBC2 12.89
Unmapped_reads 9372414
TSS_coding_score 18.1
TSS_non-coding_score 3.4
Pause_index 7.77
Plus_FRiP 0.39
Minus_FRiP 0.39
mRNA_contamination 7.26
Time 2:18:35
Success 06-15-09:35:45

K562_RNA-seq_80 objects

Links
Figures
Fig.0 Adapter insertion distribution
Fig.1 TSS enrichment
Fig.2 Pause index
Fig.3 cFRiF
Fig.4 FRiF
Fig.5 mRNA contamination