Sample name: H9_PRO-seq_1

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name H9_PRO-seq_1
sample_desc H9 PRO-seq
treatment DMSO
replicate 1
toggle 1
protocol PRO
organism human
read_type PAIRED
cell_type H9
purpose low pause index; differential analysis
umi_status true_8
umi_length 8
data_source SRA
read1 /project/shefflab/data/guertin/fastq/H9_DMSO_rep1_PE1.fastq.gz
read2 /project/shefflab/data/guertin/fastq/H9_DMSO_rep1_PE2.fastq.gz
srr H9_DMSO_rep1
Sample_title H9_DMSO_rep1
Sample_geo_accession GSM4214080
Sample_source_name_ch1 H9 cells
File_mb 2469.73
Read_type paired
Genome hg38
Raw_reads 97729860
Fastq_reads 97729860
Reads_with_adapter 34822522.0
Uninformative_adapter_reads 17998987.0
Duplicate_reads 3516802.0
Pct_uninformative_adapter_reads 36.8342
Trimmed_reads 60442686
Trim_loss_rate 38.15
Peak_adapter_insertion_size 20
Degradation_ratio 0.8896
Aligned_reads_human_rDNA 5408680.0
Alignment_rate_human_rDNA 8.95
Mapped_reads 48339851
QC_filtered_reads 27585022
Aligned_reads 20754829.0
Alignment_rate 34.34
Total_efficiency 21.24
Read_depth 3.26
Mitochondrial_reads 674956
Maximum_read_length 38
Genome_size 3099922541
Frac_exp_unique_at_10M 0.8774
NRF 1.0
PBC1 10983354.0
PBC2 10983354.0
Unmapped_reads 6258301
TSS_coding_score 26.7
TSS_non-coding_score 10.1
Pause_index 32.63
Plus_FRiP 0.38
Minus_FRiP 0.36
mRNA_contamination 1.23
Time 3:25:37
Success 02-27-12:51:09

H9_PRO-seq_1 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