gold5


Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary
sample_name gold5
sample_description ATAC-seq from dendritic cell (ENCLB384NOX)
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 SRR5210390
SRX SRX2523854
Sample_geo_accession GSM2471245
Sample_series_id GSE94173
read_type PAIRED
Sample_instrument_model Illumina HiSeq 2000
read1 /sfs/lustre/allocations/shefflab/data/sra_fastq/SRR5210390_1.fastq.gz
read2 /sfs/lustre/allocations/shefflab/data/sra_fastq/SRR5210390_2.fastq.gz
File_mb 3271.827
Read_type paired
Genome hg19
Raw_reads 104881014
Fastq_reads 104881014
Trimmed_reads 104879682
Trim_loss_rate 0.0
Aligned_reads_rCRSd_3k 19947382.0
Alignment_rate_rCRSd_3k 19.02
Aligned_reads_human_repeats 5705260.0
Alignment_rate_human_repeats 5.44
Mapped_reads 77535388
QC_filtered_reads 5833350.0
Aligned_reads 71702038
Alignment_rate 68.37
Total_efficiency 68.37
Mitochondrial_reads 8423.0
NRF 0.94
PBC1 0.97
PBC2 32.04
Unmapped_reads 1691652.0
Duplicate_reads 1246861
Dedup_aligned_reads 70455177.0
Dedup_alignment_rate 67.18
Dedup_total_efficiency 67.18
TSS_Score 13.134632225
Peak_count 116788
FRiP 0.252560310768
Time 3:00:57
Success 01-04-12:23:16