Sample name: K562_RNA-seq_90

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name K562_RNA-seq_90
sample_desc 10% K562 PRO-seq + 90% K562 RNA-seq
treatment 70M total reads
protocol PRO
organism human
read_type SINGLE
umi_len 0
read1 /project/shefflab/data//guertin/fastq/K562_90pctRNA.fastq.gz
srr K562_90pctRNA
File_mb 5212.18
Read_type SINGLE
Genome hg38
Raw_reads 70000000
Fastq_reads 70000000
Reads_with_adapter 28335107.0
Uninformative_adapter_reads 175101.0
Pct_uninformative_adapter_reads 0.2501
Trimmed_reads 69824899
Trim_loss_rate 0.25
Peak_adapter_insertion_size 34
Degradation_ratio 0.2307
Aligned_reads_human_rDNA 2091621.0
Alignment_rate_human_rDNA 3.0
Mapped_reads 57285710
QC_filtered_reads 12079693
Aligned_reads 45206017
Alignment_rate 64.74
Total_efficiency 64.58
Read_depth 9.03
Mitochondrial_reads 3902862
Maximum_read_length 100
Genome_size 3099922541
NRF 0.54
PBC1 0.83
PBC2 11.16
Unmapped_reads 10447568
TSS_coding_score 18.6
TSS_non-coding_score 3.0
Pause_index 7.62
Plus_FRiP 0.39
Minus_FRiP 0.4
mRNA_contamination 9.16
Time 2:09:26
Success 06-15-09:26:37

K562_RNA-seq_90 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