Sample name: K562_RNA-seq_40

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name K562_RNA-seq_40
sample_desc 60% K562 PRO-seq + 40% K562 RNA-seq
treatment 70M total reads
protocol PRO
organism human
read_type SINGLE
umi_len 0
read1 /project/shefflab/data//guertin/fastq/K562_40pctRNA.fastq.gz
srr K562_40pctRNA
Raw_reads 70000000
Fastq_reads 70000000
Reads_with_adapter 45723195.0
Uninformative_adapter_reads 1050230.0
Pct_uninformative_adapter_reads 1.5003
Trimmed_reads 68949770
Trim_loss_rate 1.5
Peak_adapter_insertion_size 34
Degradation_ratio 0.2309
Aligned_reads_human_rDNA 4427990.0
Alignment_rate_human_rDNA 6.42
Mapped_reads 59454882
QC_filtered_reads 9022968
Aligned_reads 50431914
Alignment_rate 73.14
Total_efficiency 72.05
Read_depth 6.34
Mitochondrial_reads 2452024
Maximum_read_length 100
Genome_size 3099922541
NRF 0.75
PBC1 0.9
PBC2 13.91
Unmapped_reads 5066898
TSS_coding_score 16.6
TSS_non-coding_score 5.0
File_mb 5584.92
Read_type SINGLE
Genome hg38
Pause_index 8.63
Plus_FRiP 0.37
Minus_FRiP 0.36
mRNA_contamination 3.53
Time 0:32:36
Success 06-14-21:44:23

K562_RNA-seq_40 objects

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