gold2


Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary
sample_name gold2
sample_description ATAC-seq from dendritic cell (ENCLB811FLK)
treatment_description Homo sapiens dendritic in vitro differentiated cells treated with 0 ng/mL Lipopolysaccharide for 0 hours
organism human
protocol ATAC-seq
data_source SRA
SRR SRR5210450
SRX SRX2523906
Sample_geo_accession GSM2471300
Sample_series_id GSE94222
read_type PAIRED
Sample_instrument_model Illumina HiSeq 2000
read1 /sfs/lustre/allocations/shefflab/data/sra_fastq/SRR5210450_1.fastq.gz
read2 /sfs/lustre/allocations/shefflab/data/sra_fastq/SRR5210450_2.fastq.gz
File_mb 1603.8181
Read_type paired
Genome hg19
Raw_reads 28408648
Fastq_reads 28408648
Trimmed_reads 28408460
Trim_loss_rate 0.0
Aligned_reads_rCRSd_3k 11074130.0
Alignment_rate_rCRSd_3k 38.98
Aligned_reads_human_repeats 1147860.0
Alignment_rate_human_repeats 4.04
Mapped_reads 16008042
QC_filtered_reads 1127526.0
Aligned_reads 14880516
Alignment_rate 52.38
Total_efficiency 52.38
Mitochondrial_reads 946.0
NRF 0.93
PBC1 0.96
PBC2 27.59
Unmapped_reads 178428.0
Duplicate_reads 271118
Dedup_aligned_reads 14609398.0
Dedup_alignment_rate 51.43
Dedup_total_efficiency 51.43
TSS_Score 12.5511477385
Peak_count 49890
FRiP 0.164292421042
Time 0:52:31
Success 01-03-15:26:21