Sample name: HEK_ARF_PRO-seq

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name HEK_ARF_PRO-seq
sample_desc HEK w/ osTIR1, ZNF143AID, ARF PRO-seq
treatment Auxin
replicate 1
toggle 1
protocol PRO
organism human
read_type PAIRED
cell_type HEK293T
purpose very degraded library (post Pol liberation)
umi_status true_8
umi_length 8
data_source SRA
read1 /project/shefflab/data/guertin/fastq/SRR8608070_PE1.fastq.gz
read2 /project/shefflab/data/guertin/fastq/SRR8608070_PE2.fastq.gz
srr SRR8608070
srx SRX5407484
Sample_title HEK_TIR1_ZNF143AID_ARF_Auxin_rep4
Sample_geo_accession GSM3618143
Sample_source_name_ch1 HEK-293T cells
Sample_characteristics_ch1 cell line: HEK-293T
File_mb 1302.45
Read_type paired
Genome hg38
Raw_reads 53049272
Fastq_reads 53049272
Reads_with_adapter 21262101.0
Uninformative_adapter_reads 8863359.0
Duplicate_reads 778059.0
Pct_uninformative_adapter_reads 33.4156
Trimmed_reads 32625384
Trim_loss_rate 38.5
Peak_adapter_insertion_size 17
Degradation_ratio 1.349
Aligned_reads_human_rDNA 3622152.0
Alignment_rate_human_rDNA 11.1
Mapped_reads 24911965
QC_filtered_reads 15309473
Aligned_reads 9602492.0
Alignment_rate 29.43
Total_efficiency 18.1
Read_depth 2.05
Mitochondrial_reads 252493
Maximum_read_length 38
Genome_size 3099922541
Frac_exp_unique_at_10M 0.9163
NRF 1.0
PBC1 5434839.0
PBC2 5434839.0
Unmapped_reads 3997391
TSS_coding_score 18.5
TSS_non-coding_score 2.4
Pause_index 17.17
Plus_FRiP 0.42
Minus_FRiP 0.39
mRNA_contamination 1.29
Time 2:23:12
Success 02-27-11:48:45

HEK_ARF_PRO-seq 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