Sample name: H9_PRO-seq_2

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name H9_PRO-seq_2
sample_desc H9 PRO-seq
treatment DMSO
protocol PRO
organism human
read_type PAIRED
umi_len 8
read1 /project/shefflab/data//guertin/fastq/H9_DMSO_rep2_PE1.fastq.gz
read2 /project/shefflab/data//guertin/fastq/H9_DMSO_rep2_PE2.fastq.gz
srr H9_DMSO_rep2
Raw_reads 115714026
Fastq_reads 115714026
File_mb 2754.18
Read_type PAIRED
Genome hg38
Reads_with_adapter 45847892.0
Uninformative_adapter_reads 28610139.0
Duplicate_reads 3047417.0
Pct_uninformative_adapter_reads 49.4497
Trimmed_reads 56658510
Trim_loss_rate 51.04
Peak_adapter_insertion_size 20
Degradation_ratio 1.0321
Aligned_reads_human_rDNA 5827176.0
Alignment_rate_human_rDNA 10.28
Mapped_reads 43719896
QC_filtered_reads 25554169
Aligned_reads 18165727.0
Alignment_rate 32.06
Total_efficiency 15.7
Read_depth 3.11
Mitochondrial_reads 840435
Maximum_read_length 38
Genome_size 3099922541
Frac_exp_unique_at_10M 0.8541
NRF 1.0
PBC1 9741100.0
PBC2 9741100.0
Unmapped_reads 6664276
TSS_coding_score 33.8
TSS_non-coding_score 12.3
Pause_index 34.0
Plus_FRiP 0.39
Minus_FRiP 0.36
mRNA_contamination 1.29
Time 2:35:29
Success 06-15-15:34:39

H9_PRO-seq_2 objects

Links
Figures
Fig.0 Adapter insertion distribution
Fig.1 Library complexity
Fig.2 TSS enrichment
Fig.3 Pause index
Fig.4 cFRiF
Fig.5 FRiF
Fig.6 mRNA contamination